psidev-pi-dev

[Psidev-pi-dev] FW: Spec doc

[Jones, A. <And...@li...>]

Hi all,

Eric has re-generated the schema documentation for us. This is getting fairly
close to a version I can cut and paste into the spec doc. Let me know if you
have any comments,

Cheers

Andy

 

 

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: 01 December 2008 09:23
To: Jones, Andy
Cc: 'Eric Deutsch'
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Andy, sorry for the delay, US holiday over here. You will find updated HTML
documentation at:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working.html

 

A version that is suitable for cut-n-paste into a word doc is at:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working_simple.html

 

I fixed some of the problems. The main problem I still know about is that in the
subelement listing, any subelements that are double-tall nested substitution
grouped elements do not have their definition visible. If one clicks on the
subelement, the main element does have a definition. So it’s there, but my
program is stymied by the various levels. This is fixable, but probably not
before submission.

 

If you send me screen-capture images to embed in some elements, that can be done
if you like.

 

If there are still other outstanding issues, please let me know

 

Regards,

Eric

 

 

 

 

________________________________

From: Jones, Andy [mailto:And...@li...] 
Sent: Thursday, November 27, 2008 4:56 AM
To: Eric Deutsch
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Eric,

 

Any chance you could look at the generated documentation this week? We’re aiming
to submit the specs to the document process by Monday...

Thanks

Andy

 

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: 21 November 2008 17:44
To: Jones, Andy
Cc: 'Eric Deutsch'
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Andy, yes, I will fix the bugs and regenerate the docs from the latest schema
and files early next week.

 

I will also have a look at TPP related materials for AnalysisXML and get back to
you.

 

Sorry I’ve missed the calls. That time is very awkward for me and I’ve
occasionally been confused by Wednesday/Thursday switches.

 

Regards,

Eric

 

 

________________________________

From: Jones, Andy [mailto:And...@li...] 
Sent: Friday, November 21, 2008 2:09 AM
To: Eric Deutsch
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Eric,

 

Would you be able to do a couple of updates to the auto-generated docs? There’s
a couple of errors to fix.

 

When there is an instance of: <xsd:element ref="pf:DatabaseReference"
minOccurs="0">, would you be able to retrieve the documentation in the table
from the referenced element.

 

Also, when an element is inherited from, documentation for inherited attributes
does not appear in the table (e.g. see Specificity rule, no docs for cvRef,
unitName etc.) – unless we were missing documentation for these attributes when
it was last generated?.

 

There are also a few instances of elements imported from the FuGE-light schema
which are completely empty, no attributes or documentation e.g. Organization or
Person.

 

We’re aiming to submit the specs to the PSI process by the end of month (i.e. a
week on Monday), so if you would be able to look at this fairly soon it would be
very much appreciated! Also, any chance that you can get someone to generate the
TPP and SpectraST examples at your end. It’s no disaster if we submit to the
process without these but it would be beneficial.

 

Cheers

Andy

 

 

 

 

 

 

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: 17 October 2008 07:43
To: psi...@li...
Subject: Re: [Psidev-pi-dev] Spec doc

 

Hi everyone, I updated the current draft of the on-line autogenerated schema
docs to the latest svn. The result is at:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working.html

 

It looks like the current mapping file is just a template without any term
mappings themselves. Just as a test, I wrote into the axml-mapping.xml file the
mapping information for SearchType and it seemed to pull it out of the CV
nicely:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working.html#SearchType

 

The autogeneration pulls examples out of one file. I randomly chose
Mascot_MSMS_example.axml. Is there a better instance document to automatically
pull examples out of?

 

Regards,

Eric

 

 

 

________________________________

From: Jones, Andy [mailto:And...@li...] 
Sent: Monday, October 13, 2008 7:07 AM
To: psi...@li...
Subject: [Psidev-pi-dev] Spec doc

 

Hi all,

 

A new version of the spec document has been uploaded by SVN (in the
specification_document directory), and previous versions have been put in a
subfolder. I think the document is getting there... 

 

Main tasks still to do:

 

-          Finish section on use cases when we have finally agreed the list
online and made all the example files.

-          Import some parts of the example files to demonstrate a few specific
points

-          Import the autogenerated documentation

 

Before we can submit, the main outstanding issues are:

 

-          CV - looking through the CV there is still a fair bit of work to do,
there’s quite a few terms with missing or incorrect documentation

-          Mapping file

-          Finish example files.

 

Prior to the call on Thurs, can we have a think about how we plan to get the CV
into shape and discuss it as a main agenda item...

 

Also new schema uploaded with a few bits of improved documentation.

Cheers

Andy

 

 

 

 

 

 

 

 

 

 

 

 

 

Re: [Psidev-pi-dev] FW: Spec doc

[David C. <dc...@ma...>]

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Hi Andy,<br>
<br>
Some minor changes:<br>
<pre>From:
&lt;pf:Person id="PERSON_DOC_OWNER" firstName="" lastName="Some Person" email=<a class="moz-txt-link-rfc2396E" href="mailto:so...@so...">"so...@so..."</a>&gt;
to:
&lt;pf:Person id="PERSON_DOC_OWNER" firstName="Some" lastName="Person" email=<a class="moz-txt-link-rfc2396E" href="mailto:so...@so...">"so...@so..."</a>&gt;


Example Context: 	
&lt;pf:cv id="PSI-PI"        fullName="PSI-PI"        URI=<a class="moz-txt-link-rfc2396E" href="http://www.psidev.info/not_sure_of_url_to_cv.obo">"http://www.psidev.info/not_sure_of_url_to_cv.obo"</a>&gt;&lt;/pf:cv&gt;
We only want the cv psidev.info when we finally release. Guess it's OK to leave this as it is at the moment.


Element &lt;AnalysisSoftware&gt;
Definition: 	A data set containing spectra data (consisting of one or more spectra). 
Definition looks like a copy and paste of something quite different!


Element &lt;pf:ContactRole&gt;
Definition: 	The Contact that provided the document instance. 
We use the contact role in several different places. Definition needs to be a bit more general? 
In the example it is for a software vendor.



Element &lt;pf:Person&gt;
Example needs filling out a bit with some fictitious person.


Element &lt;Peptide&gt;
sequenceMass xsd:double - The sum of the unmodified (poly)peptide sequence residues, exclusive of the termini masses in Daltons.
</pre>
Oh dear. Some of the examples are inclusive of the termini masses and
any modifications, others are not. In theory, it's possible to
calculate the mass given the modification delta and the CTermGain="OH"
NTermGain="H" from the enzyme. However, that's not trivial in a case of
multiple enzymes. I'd suggest we change the definition to include the
termini and mods. Martin (whose examples followed the documentation) 
may think differently?<br>
<br>
<br>
Element &lt;Inputs&gt;<br>
Definition:     The inputs to the analyses including the databases
searched and the spectral data <br>
The example shows the input file to the process that created the
analysisXML document (the Mascot .dat file)<br>
The global definition needs changing. Also, need to add a definition
for SpectraData.<br>
<br>
<br>
Element &lt;DatabaseTranslation&gt;<br>
Could take examples from Mascot_NA_example.axml<br>
<br>
<br>
Element &lt;Enzyme&gt;<br>
missedCleavages    xsd:int    optional    URI of the analysis software
e.g. manufacturer's website<br>
semiSpecific - shouldn't this be a boolean?<br>
<br>
<br>
Element &lt;PlusValue&gt;<br>
unitName    xsd:string    -    The name of the unit.<br>
Shame that it doesn't pull out the allowed CV from the mapping file:<br>
<br>
&lt;CvTerm termAccession="UO:0000221" useTermName="false"
useTerm="true" termName="dalton" cvIdentifierRef="UO" /&gt;<br>
&lt;CvTerm termAccession="UO:0000166" useTermName="false"
useTerm="false" termName="parts per notation" cvIdentifierRef="UO" /&gt;<br>
<br>
Element &lt;SpectrumIdentificationItem&gt;<br>
Has an attribute of rank and also a CV item. From the minutes here:<br>
<a class="moz-txt-link-freetext" href="http://psidev.info/index.php?q=node/380">http://psidev.info/index.php?q=node/380</a><br>
Looks as though we agreed it should be an attribute and removed from
the CV<br>
<br>
Cheers,<br>
David<br>
<br>
Jones, Andy wrote:
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  <div class="Section1">
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Hi all,<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Eric has
re-generated the schema
documentation for us. This is getting fairly close to a version I can
cut and
paste into the spec doc. Let me know if you have any comments,<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Cheers<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Andy<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <div
 style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
  <div>
  <div
 style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
  <p class="MsoNormal"><b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US">From:</span></b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"> Eric Deutsch
[<a class="moz-txt-link-freetext" href="mailto:ede...@sy...">mailto:ede...@sy...</a>] <br>
  <b>Sent:</b> 01 December 2008 09:23<br>
  <b>To:</b> Jones, Andy<br>
  <b>Cc:</b> 'Eric Deutsch'<br>
  <b>Subject:</b> RE: [Psidev-pi-dev] Spec doc<o:p></o:p></span></p>
  </div>
  </div>
  <p class="MsoNormal"><o:p> </o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US">Hi Andy, sorry for the delay, US holiday over here. You
will find
updated HTML documentation at:<o:p></o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span lang="EN-US"><a moz-do-not-send="true"
 href="http://www.peptideatlas.org/tmp/AnalysisXML_working.html">http://www.peptideatlas.org/tmp/AnalysisXML_working.html</a><o:p></o:p></span></p>
  <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span lang="EN-US">A version that is suitable
for cut-n-paste
into a word doc is at:</span><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"><o:p></o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span lang="EN-US"><a moz-do-not-send="true"
 href="http://www.peptideatlas.org/tmp/AnalysisXML_working_simple.html">http://www.peptideatlas.org/tmp/AnalysisXML_working_simple.html</a><o:p></o:p></span></p>
  <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span lang="EN-US">I fixed some of the problems.
The main
problem I still know about is that in the subelement listing, any
subelements
that are double-tall nested substitution grouped elements do not have
their
definition visible. If one clicks on the subelement, the main element
does have
a definition. So it’s there, but my program is stymied by the various
levels.
This is fixable, but probably not before submission.<o:p></o:p></span></p>
  <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span lang="EN-US">If you send me screen-capture
images to
embed in some elements, that can be done if you like.<o:p></o:p></span></p>
  <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span lang="EN-US">If there are still other
outstanding
issues, please let me know<o:p></o:p></span></p>
  <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span lang="EN-US">Regards,<o:p></o:p></span></p>
  <p class="MsoNormal"><span lang="EN-US">Eric<o:p></o:p></span></p>
  <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"><o:p> </o:p></span></p>
  <div
 style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
  <div>
  <div class="MsoNormal" style="text-align: center;" align="center"><span
 style="font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"
 lang="EN-US">
  <hr align="center" size="2" width="100%"></span></div>
  <p class="MsoNormal"><b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US">From:</span></b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"> Jones, Andy [<a class="moz-txt-link-freetext" href="mailto:And...@li...">mailto:And...@li...</a>]
  <br>
  <b>Sent:</b> Thursday, November 27, 2008 4:56 AM<br>
  <b>To:</b> Eric Deutsch<br>
  <b>Subject:</b> RE: [Psidev-pi-dev] Spec doc</span><span
 style="font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"
 lang="EN-US"><o:p></o:p></span></p>
  </div>
  <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Hi Eric,<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Any
chance you could look at the
generated documentation this week? We’re aiming to submit the specs to
the document
process by Monday...<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Thanks<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Andy<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <div
 style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
  <div>
  <div
 style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
  <p class="MsoNormal"><b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US">From:</span></b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"> Eric Deutsch
[<a class="moz-txt-link-freetext" href="mailto:ede...@sy...">mailto:ede...@sy...</a>] <br>
  <b>Sent:</b> 21 November 2008 17:44<br>
  <b>To:</b> Jones, Andy<br>
  <b>Cc:</b> 'Eric Deutsch'<br>
  <b>Subject:</b> RE: [Psidev-pi-dev] Spec doc<o:p></o:p></span></p>
  </div>
  </div>
  <p class="MsoNormal"><o:p> </o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US">Hi Andy, yes, I will fix the bugs and regenerate the docs
from the
latest schema and files early next week.<o:p></o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US">I will also have a look at TPP related materials for
AnalysisXML
and get back to you.<o:p></o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US">Sorry I’ve missed the calls. That time is very awkward
for me and
I’ve occasionally been confused by Wednesday/Thursday switches.<o:p></o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US">Regards,<o:p></o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US">Eric<o:p></o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"><o:p> </o:p></span></p>
  <div
 style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
  <div>
  <div class="MsoNormal" style="text-align: center;" align="center"><span
 style="font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"
 lang="EN-US">
  <hr align="center" size="2" width="100%"></span></div>
  <p class="MsoNormal"><b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US">From:</span></b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"> Jones, Andy
[<a class="moz-txt-link-freetext" href="mailto:And...@li...">mailto:And...@li...</a>] <br>
  <b>Sent:</b> Friday, November 21, 2008 2:09 AM<br>
  <b>To:</b> Eric Deutsch<br>
  <b>Subject:</b> RE: [Psidev-pi-dev] Spec doc</span><span
 style="font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"
 lang="EN-US"><o:p></o:p></span></p>
  </div>
  <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Hi Eric,<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Would you
be able to do a couple
of updates to the auto-generated docs? There’s a couple of errors to
fix.<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">When
there is an instance of:
&lt;xsd:element ref="pf:DatabaseReference"
minOccurs="0"&gt;, would you be able to retrieve the documentation in
the table from the referenced element.<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Also,
when an element is
inherited from, documentation for inherited attributes does not appear
in the
table (e.g. see Specificity rule, no docs for cvRef, unitName etc.) –
unless we
were missing documentation for these attributes when it was last
generated?.<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">There are
also a few instances
of elements imported from the FuGE-light schema which are completely
empty, no
attributes or documentation e.g. Organization or Person.<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">We’re
aiming to submit the specs
to the PSI process by the end of month (i.e. a week on Monday), so if
you would
be able to look at this fairly soon it would be very much appreciated!
Also,
any chance that you can get someone to generate the TPP and SpectraST
examples
at your end. It’s no disaster if we submit to the process without these
but it
would be beneficial.<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Cheers<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Andy<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <div
 style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
  <div>
  <div
 style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
  <p class="MsoNormal"><b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US">From:</span></b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"> Eric Deutsch
[<a class="moz-txt-link-freetext" href="mailto:ede...@sy...">mailto:ede...@sy...</a>] <br>
  <b>Sent:</b> 17 October 2008 07:43<br>
  <b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a><br>
  <b>Subject:</b> Re: [Psidev-pi-dev] Spec doc<o:p></o:p></span></p>
  </div>
  </div>
  <p class="MsoNormal"><o:p> </o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US">Hi everyone, I updated the current draft of the on-line
autogenerated schema docs to the latest svn. The result is at:<o:p></o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"><a moz-do-not-send="true"
 href="http://www.peptideatlas.org/tmp/AnalysisXML_working.html">http://www.peptideatlas.org/tmp/AnalysisXML_working.html</a><o:p></o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;;"
 lang="EN-US">It
looks like the current mapping file is just a template without any term
mappings themselves. Just as a test, I wrote into the axml-mapping.xml
file the
mapping information for SearchType and it seemed to pull it out of the
CV
nicely:<o:p></o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"><a moz-do-not-send="true"
 href="http://www.peptideatlas.org/tmp/AnalysisXML_working.html#SearchType">http://www.peptideatlas.org/tmp/AnalysisXML_working.html#SearchType</a><o:p></o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;;"
 lang="EN-US">The
autogeneration pulls examples out of one file. I randomly chose
Mascot_MSMS_example.axml. Is there a better instance document to
automatically
pull examples out of?<o:p></o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;;"
 lang="EN-US">Regards,<o:p></o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;;"
 lang="EN-US">Eric<o:p></o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"><o:p> </o:p></span></p>
  <div
 style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
  <div>
  <div class="MsoNormal" style="text-align: center;" align="center"><span
 style="font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"
 lang="EN-US">
  <hr align="center" size="2" width="100%"></span></div>
  <p class="MsoNormal"><b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US">From:</span></b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"> Jones, Andy
[<a class="moz-txt-link-freetext" href="mailto:And...@li...">mailto:And...@li...</a>] <br>
  <b>Sent:</b> Monday, October 13, 2008 7:07 AM<br>
  <b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a><br>
  <b>Subject:</b> [Psidev-pi-dev] Spec doc</span><span
 style="font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"
 lang="EN-US"><o:p></o:p></span></p>
  </div>
  <p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal">Hi all,<o:p></o:p></p>
  <p class="MsoNormal"><o:p> </o:p></p>
  <p class="MsoNormal">A new version of the spec document has been
uploaded by SVN
(in the specification_document directory), and previous versions have
been put
in a subfolder. I think the document is getting there... <o:p></o:p></p>
  <p class="MsoNormal"><o:p> </o:p></p>
  <p class="MsoNormal">Main tasks still to do:<o:p></o:p></p>
  <p class="MsoNormal"><o:p> </o:p></p>
  <p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
 style="">-<span
 style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">         
  </span></span><!--[endif]-->Finish section on use cases when we have
finally agreed
the list online and made all the example files.<o:p></o:p></p>
  <p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
 style="">-<span
 style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">         
  </span></span><!--[endif]-->Import some parts of the example files to
demonstrate a
few specific points<o:p></o:p></p>
  <p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
 style="">-<span
 style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">         
  </span></span><!--[endif]-->Import the autogenerated documentation<o:p></o:p></p>
  <p class="MsoNormal"><o:p> </o:p></p>
  <p class="MsoNormal">Before we can submit, the main outstanding
issues are:<o:p></o:p></p>
  <p class="MsoNormal"><o:p> </o:p></p>
  <p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
 style="">-<span
 style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">         
  </span></span><!--[endif]-->CV - looking through the CV there is
still a fair bit
of work to do, there’s quite a few terms with missing or incorrect
documentation<o:p></o:p></p>
  <p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
 style="">-<span
 style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">         
  </span></span><!--[endif]-->Mapping file<o:p></o:p></p>
  <p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
 style="">-<span
 style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">         
  </span></span><!--[endif]-->Finish example files.<o:p></o:p></p>
  <p class="MsoNormal"><o:p> </o:p></p>
  <p class="MsoNormal">Prior to the call on Thurs, can we have a think
about how we
plan to get the CV into shape and discuss it as a main agenda item...<o:p></o:p></p>
  <p class="MsoNormal"><o:p> </o:p></p>
  <p class="MsoNormal">Also new schema uploaded with a few bits of
improved
documentation.<o:p></o:p></p>
  <p class="MsoNormal">Cheers<o:p></o:p></p>
  <p class="MsoNormal">Andy<o:p></o:p></p>
  <p class="MsoNormal"><o:p> </o:p></p>
  <p class="MsoNormal"><o:p> </o:p></p>
  <p class="MsoNormal"><o:p> </o:p></p>
  <p class="MsoNormal"><o:p> </o:p></p>
  <p class="MsoNormal"><o:p> </o:p></p>
  <p class="MsoNormal" style="margin-left: 18pt;"><o:p> </o:p></p>
  <p class="MsoNormal"><o:p> </o:p></p>
  <p class="MsoNormal"><o:p> </o:p></p>
  <p class="MsoNormal"><o:p> </o:p></p>
  <p class="MsoNormal"><o:p> </o:p></p>
  <p class="MsoNormal"><o:p> </o:p></p>
  <p class="MsoNormal"><o:p> </o:p></p>
  <p class="MsoNormal"><o:p> </o:p></p>
  </div>
  </div>
  </div>
  </div>
  </div>
  </div>
  </div>
  <pre wrap="">
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  <pre wrap="">
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_______________________________________________
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<a class="moz-txt-link-abbreviated" href="mailto:Psi...@li...">Psi...@li...</a>
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  </pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">-- 
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344

<a class="moz-txt-link-abbreviated" href="mailto:dc...@ma...">dc...@ma...</a>
<a class="moz-txt-link-freetext" href="http://www.matrixscience.com">http://www.matrixscience.com</a>

Matrix Science Ltd. is registered in England and Wales
Company number 3533898</pre>
</body>
</html>

Re: [Psidev-pi-dev] FW: Spec doc

[Eric D. <ede...@sy...>]

Hi everyone, I have just updated the HTML and plain documentation files
based on what's in SVN right now.

 

I have fixed the missing definition problem.

 

I have added some embedded figures that Any sent.

 

I should mention that I am using Mascot_MSMS_example.axml as the example
template. What my software does is reads one example file and then injects
examples from that file into the documentation. I picked this file somewhat
arbitrarily. If there is a better file, please let me know. The longest file
is not necessarily best. But rather the file that exercises most parts of
the format is best. Anyone have a better suggestion? Maybe I could adjust my
program to read several files and try to automatically pick the "best"
example from any of those files

 

Regarding David's comment about <PlusValue> below.. it seems you currently
have:

  <PlusValue  unitCvRef="UO" unitAccession="UO:0000221" unitName="dalton"
value="0.5" />

If this were:

  <PlusValue>

    <pf:cvParam accession="UO:0000221" name="dalton" value="0.5" cvRef="UO"
/>

  </PlusValue>

 

Then my software would display what you expect. Is there a compelling reason
why you use the former instead of the latter? It would seem that the latter
is more generic from a software-handling perspective.

 

Or, even better, the more mzML style would be:

 

<pf:cvParam accession="PI:00999" name="search window plus value" value="0.5"
cvRef="PSI-PI"

unitAccession="UO:0000221" name="dalton" cvRef="UO" />

 

Just causing trouble.

Eric

 

 

 

  _____  

From: David Creasy [mailto:dc...@ma...] 
Sent: Monday, December 01, 2008 9:41 AM
To: psi...@li...
Subject: Re: [Psidev-pi-dev] FW: Spec doc

 

Hi Andy,

Some minor changes:

From:
<pf:Person id="PERSON_DOC_OWNER" firstName="" lastName="Some Person" email=
<mailto:so...@so...> "so...@so...">
to:
<pf:Person id="PERSON_DOC_OWNER" firstName="Some" lastName="Person" email=
<mailto:so...@so...> "so...@so...">
 
 
Example Context:      
<pf:cv id="PSI-PI"        fullName="PSI-PI"        URI=
<http://www.psidev.info/not_sure_of_url_to_cv.obo>
"http://www.psidev.info/not_sure_of_url_to_cv.obo"></pf:cv>
We only want the cv psidev.info when we finally release. Guess it's OK to
leave this as it is at the moment.
 
 
Element <AnalysisSoftware>
Definition:   A data set containing spectra data (consisting of one or more
spectra). 
Definition looks like a copy and paste of something quite different!
 
 
Element <pf:ContactRole>
Definition:   The Contact that provided the document instance. 
We use the contact role in several different places. Definition needs to be
a bit more general? 
In the example it is for a software vendor.
 
 
 
Element <pf:Person>
Example needs filling out a bit with some fictitious person.
 
 
Element <Peptide>
sequenceMass xsd:double - The sum of the unmodified (poly)peptide sequence
residues, exclusive of the termini masses in Daltons.

Oh dear. Some of the examples are inclusive of the termini masses and any
modifications, others are not. In theory, it's possible to calculate the
mass given the modification delta and the CTermGain="OH" NTermGain="H" from
the enzyme. However, that's not trivial in a case of multiple enzymes. I'd
suggest we change the definition to include the termini and mods. Martin
(whose examples followed the documentation)  may think differently?


Element <Inputs>
Definition:     The inputs to the analyses including the databases searched
and the spectral data 
The example shows the input file to the process that created the analysisXML
document (the Mascot .dat file)
The global definition needs changing. Also, need to add a definition for
SpectraData.


Element <DatabaseTranslation>
Could take examples from Mascot_NA_example.axml


Element <Enzyme>
missedCleavages    xsd:int    optional    URI of the analysis software e.g.
manufacturer's website
semiSpecific - shouldn't this be a boolean?


Element <PlusValue>
unitName    xsd:string    -    The name of the unit.
Shame that it doesn't pull out the allowed CV from the mapping file:

<CvTerm termAccession="UO:0000221" useTermName="false" useTerm="true"
termName="dalton" cvIdentifierRef="UO" />
<CvTerm termAccession="UO:0000166" useTermName="false" useTerm="false"
termName="parts per notation" cvIdentifierRef="UO" />

Element <SpectrumIdentificationItem>
Has an attribute of rank and also a CV item. From the minutes here:
http://psidev.info/index.php?q=node/380
Looks as though we agreed it should be an attribute and removed from the CV

Cheers,
David

Jones, Andy wrote: 

Hi all,

Eric has re-generated the schema documentation for us. This is getting
fairly close to a version I can cut and paste into the spec doc. Let me know
if you have any comments,

Cheers

Andy

 

 

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: 01 December 2008 09:23
To: Jones, Andy
Cc: 'Eric Deutsch'
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Andy, sorry for the delay, US holiday over here. You will find updated
HTML documentation at:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working.html

 

A version that is suitable for cut-n-paste into a word doc is at:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working_simple.html

 

I fixed some of the problems. The main problem I still know about is that in
the subelement listing, any subelements that are double-tall nested
substitution grouped elements do not have their definition visible. If one
clicks on the subelement, the main element does have a definition. So it's
there, but my program is stymied by the various levels. This is fixable, but
probably not before submission.

 

If you send me screen-capture images to embed in some elements, that can be
done if you like.

 

If there are still other outstanding issues, please let me know

 

Regards,

Eric

 

 

 

 

  _____  

From: Jones, Andy [mailto:And...@li...] 
Sent: Thursday, November 27, 2008 4:56 AM
To: Eric Deutsch
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Eric,

 

Any chance you could look at the generated documentation this week? We're
aiming to submit the specs to the document process by Monday...

Thanks

Andy

 

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: 21 November 2008 17:44
To: Jones, Andy
Cc: 'Eric Deutsch'
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Andy, yes, I will fix the bugs and regenerate the docs from the latest
schema and files early next week.

 

I will also have a look at TPP related materials for AnalysisXML and get
back to you.

 

Sorry I've missed the calls. That time is very awkward for me and I've
occasionally been confused by Wednesday/Thursday switches.

 

Regards,

Eric

 

 

  _____  

From: Jones, Andy [mailto:And...@li...] 
Sent: Friday, November 21, 2008 2:09 AM
To: Eric Deutsch
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Eric,

 

Would you be able to do a couple of updates to the auto-generated docs?
There's a couple of errors to fix.

 

When there is an instance of: <xsd:element ref="pf:DatabaseReference"
minOccurs="0">, would you be able to retrieve the documentation in the table
from the referenced element.

 

Also, when an element is inherited from, documentation for inherited
attributes does not appear in the table (e.g. see Specificity rule, no docs
for cvRef, unitName etc.) - unless we were missing documentation for these
attributes when it was last generated?.

 

There are also a few instances of elements imported from the FuGE-light
schema which are completely empty, no attributes or documentation e.g.
Organization or Person.

 

We're aiming to submit the specs to the PSI process by the end of month
(i.e. a week on Monday), so if you would be able to look at this fairly soon
it would be very much appreciated! Also, any chance that you can get someone
to generate the TPP and SpectraST examples at your end. It's no disaster if
we submit to the process without these but it would be beneficial.

 

Cheers

Andy

 

 

 

 

 

 

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: 17 October 2008 07:43
To: psi...@li...
Subject: Re: [Psidev-pi-dev] Spec doc

 

Hi everyone, I updated the current draft of the on-line autogenerated schema
docs to the latest svn. The result is at:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working.html

 

It looks like the current mapping file is just a template without any term
mappings themselves. Just as a test, I wrote into the axml-mapping.xml file
the mapping information for SearchType and it seemed to pull it out of the
CV nicely:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working.html#SearchType

 

The autogeneration pulls examples out of one file. I randomly chose
Mascot_MSMS_example.axml. Is there a better instance document to
automatically pull examples out of?

 

Regards,

Eric

 

 

 

  _____  

From: Jones, Andy [mailto:And...@li...] 
Sent: Monday, October 13, 2008 7:07 AM
To: psi...@li...
Subject: [Psidev-pi-dev] Spec doc

 

Hi all,

 

A new version of the spec document has been uploaded by SVN (in the
specification_document directory), and previous versions have been put in a
subfolder. I think the document is getting there... 

 

Main tasks still to do:

 

Finish section on use cases when we have finally agreed the list online and
made all the example files.

Import some parts of the example files to demonstrate a few specific points

Import the autogenerated documentation

 

Before we can submit, the main outstanding issues are:

 

CV - looking through the CV there is still a fair bit of work to do, there's
quite a few terms with missing or incorrect documentation

Mapping file

Finish example files.

 

Prior to the call on Thurs, can we have a think about how we plan to get the
CV into shape and discuss it as a main agenda item...

 

Also new schema uploaded with a few bits of improved documentation.

Cheers

Andy

 

 

 

 

 

 

 

 

 

 

 

 

 

 





  _____  



 
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great
prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100
<http://moblin-contest.org/redirect.php?banner_id=100&url=/> &url=/
 





  _____  



 
_______________________________________________
Psidev-pi-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
  





-- 
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344
 
dc...@ma...
http://www.matrixscience.com
 
Matrix Science Ltd. is registered in England and Wales
Company number 3533898

Re: [Psidev-pi-dev] FW: Spec doc

[Pierre-Alain B. <pie...@is...>]

Hi,

David Creasy wrote:
> Hi Andy,
>
> Some minor changes:
> From:
> <pf:Person id="PERSON_DOC_OWNER" firstName="" lastName="Some Person" email="so...@so...">
> to:
> <pf:Person id="PERSON_DOC_OWNER" firstName="Some" lastName="Person" email="so...@so...">
>
>
> Example Context: 	
> <pf:cv id="PSI-PI"        fullName="PSI-PI"        URI=*MailScanner has detected a possible fraud attempt from "www.psidev.info" claiming to be* "http://www.psidev.info/not_sure_of_url_to_cv.obo"></pf:cv>
> We only want the cv psidev.info when we finally release. Guess it's OK to leave this as it is at the moment.
>
>
> Element <AnalysisSoftware>
> Definition: 	A data set containing spectra data (consisting of one or more spectra). 
> Definition looks like a copy and paste of something quite different!
>
>
> Element <pf:ContactRole>
> Definition: 	The Contact that provided the document instance. 
> We use the contact role in several different places. Definition needs to be a bit more general? 
> In the example it is for a software vendor.
>
>
>
> Element <pf:Person>
> Example needs filling out a bit with some fictitious person.
>
>
> Element <Peptide>
> sequenceMass xsd:double - The sum of the unmodified (poly)peptide sequence residues, exclusive of the termini masses in Daltons.
>   
> Oh dear. Some of the examples are inclusive of the termini masses and 
> any modifications, others are not. In theory, it's possible to 
> calculate the mass given the modification delta and the CTermGain="OH" 
> NTermGain="H" from the enzyme. However, that's not trivial in a case 
> of multiple enzymes. I'd suggest we change the definition to include 
> the termini and mods. Martin (whose examples followed the 
> documentation)  may think differently?
I aggree: with termini and mods. Calculated neutral mass in Da (not 
m/z), monoisotopic, 6digits after unit?
>
>
> Element <Inputs>
> Definition:     The inputs to the analyses including the databases 
> searched and the spectral data
> The example shows the input file to the process that created the 
> analysisXML document (the Mascot .dat file)
> The global definition needs changing. Also, need to add a definition 
> for SpectraData.
>
>
> Element <DatabaseTranslation>
> Could take examples from Mascot_NA_example.axml
>
>
> Element <Enzyme>
> missedCleavages    xsd:int    optional    URI of the analysis software 
> e.g. manufacturer's website
> semiSpecific - shouldn't this be a boolean?
>
>
> Element <PlusValue>
> unitName    xsd:string    -    The name of the unit.
> Shame that it doesn't pull out the allowed CV from the mapping file:
>
> <CvTerm termAccession="UO:0000221" useTermName="false" useTerm="true" 
> termName="dalton" cvIdentifierRef="UO" />
> <CvTerm termAccession="UO:0000166" useTermName="false" useTerm="false" 
> termName="parts per notation" cvIdentifierRef="UO" />
>
> Element <SpectrumIdentificationItem>
> Has an attribute of rank and also a CV item. From the minutes here:
> http://psidev.info/index.php?q=node/380
> Looks as though we agreed it should be an attribute and removed from 
> the CV
>
> Cheers,
> David
>
> Jones, Andy wrote:
>>
>> Hi all,
>>
>> Eric has re-generated the schema documentation for us. This is 
>> getting fairly close to a version I can cut and paste into the spec 
>> doc. Let me know if you have any comments,
>>
>> Cheers
>>
>> Andy
>>
>>  
>>
>>  
>>
>> *From:* Eric Deutsch [mailto:ede...@sy...]
>> *Sent:* 01 December 2008 09:23
>> *To:* Jones, Andy
>> *Cc:* 'Eric Deutsch'
>> *Subject:* RE: [Psidev-pi-dev] Spec doc
>>
>>  
>>
>> Hi Andy, sorry for the delay, US holiday over here. You will find 
>> updated HTML documentation at:
>>
>>  
>>
>> http://www.peptideatlas.org/tmp/AnalysisXML_working.html
>>
>>  
>>
>> A version that is suitable for cut-n-paste into a word doc is at:
>>
>>  
>>
>> http://www.peptideatlas.org/tmp/AnalysisXML_working_simple.html
>>
>>  
>>
>> I fixed some of the problems. The main problem I still know about is 
>> that in the subelement listing, any subelements that are double-tall 
>> nested substitution grouped elements do not have their definition 
>> visible. If one clicks on the subelement, the main element does have 
>> a definition. So it’s there, but my program is stymied by the various 
>> levels. This is fixable, but probably not before submission.
>>
>>  
>>
>> If you send me screen-capture images to embed in some elements, that 
>> can be done if you like.
>>
>>  
>>
>> If there are still other outstanding issues, please let me know
>>
>>  
>>
>> Regards,
>>
>> Eric
>>
>>  
>>
>>  
>>
>>  
>>
>>  
>>
>> ------------------------------------------------------------------------
>>
>> *From:* Jones, Andy [mailto:And...@li...]
>> *Sent:* Thursday, November 27, 2008 4:56 AM
>> *To:* Eric Deutsch
>> *Subject:* RE: [Psidev-pi-dev] Spec doc
>>
>>  
>>
>> Hi Eric,
>>
>>  
>>
>> Any chance you could look at the generated documentation this week? 
>> We’re aiming to submit the specs to the document process by Monday...
>>
>> Thanks
>>
>> Andy
>>
>>  
>>
>> *From:* Eric Deutsch [mailto:ede...@sy...]
>> *Sent:* 21 November 2008 17:44
>> *To:* Jones, Andy
>> *Cc:* 'Eric Deutsch'
>> *Subject:* RE: [Psidev-pi-dev] Spec doc
>>
>>  
>>
>> Hi Andy, yes, I will fix the bugs and regenerate the docs from the 
>> latest schema and files early next week.
>>
>>  
>>
>> I will also have a look at TPP related materials for AnalysisXML and 
>> get back to you.
>>
>>  
>>
>> Sorry I’ve missed the calls. That time is very awkward for me and 
>> I’ve occasionally been confused by Wednesday/Thursday switches.
>>
>>  
>>
>> Regards,
>>
>> Eric
>>
>>  
>>
>>  
>>
>> ------------------------------------------------------------------------
>>
>> *From:* Jones, Andy [mailto:And...@li...]
>> *Sent:* Friday, November 21, 2008 2:09 AM
>> *To:* Eric Deutsch
>> *Subject:* RE: [Psidev-pi-dev] Spec doc
>>
>>  
>>
>> Hi Eric,
>>
>>  
>>
>> Would you be able to do a couple of updates to the auto-generated 
>> docs? There’s a couple of errors to fix.
>>
>>  
>>
>> When there is an instance of: <xsd:element ref="pf:DatabaseReference" 
>> minOccurs="0">, would you be able to retrieve the documentation in 
>> the table from the referenced element.
>>
>>  
>>
>> Also, when an element is inherited from, documentation for inherited 
>> attributes does not appear in the table (e.g. see Specificity rule, 
>> no docs for cvRef, unitName etc.) – unless we were missing 
>> documentation for these attributes when it was last generated?.
>>
>>  
>>
>> There are also a few instances of elements imported from the 
>> FuGE-light schema which are completely empty, no attributes or 
>> documentation e.g. Organization or Person.
>>
>>  
>>
>> We’re aiming to submit the specs to the PSI process by the end of 
>> month (i.e. a week on Monday), so if you would be able to look at 
>> this fairly soon it would be very much appreciated! Also, any chance 
>> that you can get someone to generate the TPP and SpectraST examples 
>> at your end. It’s no disaster if we submit to the process without 
>> these but it would be beneficial.
>>
>>  
>>
>> Cheers
>>
>> Andy
>>
>>  
>>
>>  
>>
>>  
>>
>>  
>>
>>  
>>
>>  
>>
>> *From:* Eric Deutsch [mailto:ede...@sy...]
>> *Sent:* 17 October 2008 07:43
>> *To:* psi...@li...
>> *Subject:* Re: [Psidev-pi-dev] Spec doc
>>
>>  
>>
>> Hi everyone, I updated the current draft of the on-line autogenerated 
>> schema docs to the latest svn. The result is at:
>>
>>  
>>
>> http://www.peptideatlas.org/tmp/AnalysisXML_working.html
>>
>>  
>>
>> It looks like the current mapping file is just a template without any 
>> term mappings themselves. Just as a test, I wrote into the 
>> axml-mapping.xml file the mapping information for SearchType and it 
>> seemed to pull it out of the CV nicely:
>>
>>  
>>
>> http://www.peptideatlas.org/tmp/AnalysisXML_working.html#SearchType
>>
>>  
>>
>> The autogeneration pulls examples out of one file. I randomly chose 
>> Mascot_MSMS_example.axml. Is there a better instance document to 
>> automatically pull examples out of?
>>
>>  
>>
>> Regards,
>>
>> Eric
>>
>>  
>>
>>  
>>
>>  
>>
>> ------------------------------------------------------------------------
>>
>> *From:* Jones, Andy [mailto:And...@li...]
>> *Sent:* Monday, October 13, 2008 7:07 AM
>> *To:* psi...@li...
>> *Subject:* [Psidev-pi-dev] Spec doc
>>
>>  
>>
>> Hi all,
>>
>>  
>>
>> A new version of the spec document has been uploaded by SVN (in the 
>> specification_document directory), and previous versions have been 
>> put in a subfolder. I think the document is getting there...
>>
>>  
>>
>> Main tasks still to do:
>>
>>  
>>
>> -          Finish section on use cases when we have finally agreed 
>> the list online and made all the example files.
>>
>> -          Import some parts of the example files to demonstrate a 
>> few specific points
>>
>> -          Import the autogenerated documentation
>>
>>  
>>
>> Before we can submit, the main outstanding issues are:
>>
>>  
>>
>> -          CV - looking through the CV there is still a fair bit of 
>> work to do, there’s quite a few terms with missing or incorrect 
>> documentation
>>
>> -          Mapping file
>>
>> -          Finish example files.
>>
>>  
>>
>> Prior to the call on Thurs, can we have a think about how we plan to 
>> get the CV into shape and discuss it as a main agenda item...
>>
>>  
>>
>> Also new schema uploaded with a few bits of improved documentation.
>>
>> Cheers
>>
>> Andy
>>
>>  
>>
>>  
>>
>>  
>>
>>  
>>
>>  
>>
>>  
>>
>>  
>>
>>  
>>
>>  
>>
>>  
>>
>>  
>>
>>  
>>
>>  
>>
>> ------------------------------------------------------------------------
>>
>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
>> Build the coolest Linux based applications with Moblin SDK & win great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Psidev-pi-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
>>   
>
> -- 
> David Creasy
> Matrix Science
> 64 Baker Street
> London W1U 7GB, UK
> Tel: +44 (0)20 7486 1050
> Fax: +44 (0)20 7224 1344
>
> dc...@ma...
> http://www.matrixscience.com
>
> Matrix Science Ltd. is registered in England and Wales
> Company number 3533898
> ------------------------------------------------------------------------
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> ------------------------------------------------------------------------
>
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
>   

Re: [Psidev-pi-dev] FW: Spec doc

[Jones, A. <And...@li...>]

Hi David,

 

The changes relating the instance docs are coming from the Mascot MS/MS example
so these are for you to fix ;-)

 

Eric, are you able to import certain parts of the instance docs from other
examples. Element <DatabaseTranslation> could take examples from
Mascot_NA_example.axml? 

 

I’ll make the other recommended changes to the XSD documentation (some of these
require a fix to the generating script, which I’ve flagged to Eric separately).

 

Martin, are you happy for us to make the change relating to peptide mass
documentation (see below).

 

>semiSpecific - shouldn't this be a boolean?

 

Agreed, I’ll make this change.

 

><PlusValue>

 

Eric is right to query this part of the schema. In fact, we’ve used the
PropertyValue element only for PlusValue and MinusValue in the entire schema.
Let’s make these CV terms:

 

<pf:cvParam accession="PI:00999" name="search tolerance plus value" value=”0.5”
cvRef="PSI-PI"

unitAccession="UO:0000221" name="dalton" cvRef="UO" />

 

Andreas can you add: “search tolerance plus value” and “search tolerance minus
value” to the CV and mapping file and I’ll change the schema, does this seem
reasonable to everyone…?

 

Getting there…

 

Cheers

Andy

 

 

 

 

From: Pierre-Alain Binz [mailto:pie...@is...] 
Sent: 02 December 2008 11:17
To: David Creasy
Cc: psi...@li...
Subject: Re: [Psidev-pi-dev] FW: Spec doc

 

Hi,

David Creasy wrote: 

Hi Andy,

Some minor changes:

From:
<pf:Person id="PERSON_DOC_OWNER" firstName="" lastName="Some Person"
email="so...@so..." <mailto:so...@so...> >
to:
<pf:Person id="PERSON_DOC_OWNER" firstName="Some" lastName="Person"
email="so...@so..." <mailto:so...@so...> >
 
 
Example Context:      
<pf:cv id="PSI-PI"        fullName="PSI-PI"        URI=MailScanner has detected
a possible fraud attempt from "www.psidev.info" claiming to be
"http://www.psidev.info/not_sure_of_url_to_cv.obo"
<http://www.psidev.info/not_sure_of_url_to_cv.obo> ></pf:cv>
We only want the cv psidev.info when we finally release. Guess it's OK to leave
this as it is at the moment.
 
 
Element <AnalysisSoftware>
Definition:   A data set containing spectra data (consisting of one or more
spectra). 
Definition looks like a copy and paste of something quite different!
 
 
Element <pf:ContactRole>
Definition:   The Contact that provided the document instance. 
We use the contact role in several different places. Definition needs to be a
bit more general? 
In the example it is for a software vendor.
 
 
 
Element <pf:Person>
Example needs filling out a bit with some fictitious person.
 
 
Element <Peptide>
sequenceMass xsd:double - The sum of the unmodified (poly)peptide sequence
residues, exclusive of the termini masses in Daltons.
  

Oh dear. Some of the examples are inclusive of the termini masses and any
modifications, others are not. In theory, it's possible to calculate the mass
given the modification delta and the CTermGain="OH" NTermGain="H" from the
enzyme. However, that's not trivial in a case of multiple enzymes. I'd suggest
we change the definition to include the termini and mods. Martin (whose examples
followed the documentation)  may think differently?

I aggree: with termini and mods. Calculated neutral mass in Da (not m/z),
monoisotopic, 6digits after unit?





Element <Inputs>
Definition:     The inputs to the analyses including the databases searched and
the spectral data 
The example shows the input file to the process that created the analysisXML
document (the Mascot .dat file)
The global definition needs changing. Also, need to add a definition for
SpectraData.


Element <DatabaseTranslation>
Could take examples from Mascot_NA_example.axml


Element <Enzyme>
missedCleavages    xsd:int    optional    URI of the analysis software e.g.
manufacturer's website
semiSpecific - shouldn't this be a boolean?


Element <PlusValue>
unitName    xsd:string    -    The name of the unit.
Shame that it doesn't pull out the allowed CV from the mapping file:

<CvTerm termAccession="UO:0000221" useTermName="false" useTerm="true"
termName="dalton" cvIdentifierRef="UO" />
<CvTerm termAccession="UO:0000166" useTermName="false" useTerm="false"
termName="parts per notation" cvIdentifierRef="UO" />

Element <SpectrumIdentificationItem>
Has an attribute of rank and also a CV item. From the minutes here:
http://psidev.info/index.php?q=node/380
Looks as though we agreed it should be an attribute and removed from the CV

Cheers,
David

Jones, Andy wrote: 

Hi all,

Eric has re-generated the schema documentation for us. This is getting fairly
close to a version I can cut and paste into the spec doc. Let me know if you
have any comments,

Cheers

Andy

 

 

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: 01 December 2008 09:23
To: Jones, Andy
Cc: 'Eric Deutsch'
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Andy, sorry for the delay, US holiday over here. You will find updated HTML
documentation at:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working.html

 

A version that is suitable for cut-n-paste into a word doc is at:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working_simple.html

 

I fixed some of the problems. The main problem I still know about is that in the
subelement listing, any subelements that are double-tall nested substitution
grouped elements do not have their definition visible. If one clicks on the
subelement, the main element does have a definition. So it’s there, but my
program is stymied by the various levels. This is fixable, but probably not
before submission.

 

If you send me screen-capture images to embed in some elements, that can be done
if you like.

 

If there are still other outstanding issues, please let me know

 

Regards,

Eric

 

 

 

 

________________________________

From: Jones, Andy [mailto:And...@li...] 
Sent: Thursday, November 27, 2008 4:56 AM
To: Eric Deutsch
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Eric,

 

Any chance you could look at the generated documentation this week? We’re aiming
to submit the specs to the document process by Monday...

Thanks

Andy

 

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: 21 November 2008 17:44
To: Jones, Andy
Cc: 'Eric Deutsch'
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Andy, yes, I will fix the bugs and regenerate the docs from the latest schema
and files early next week.

 

I will also have a look at TPP related materials for AnalysisXML and get back to
you.

 

Sorry I’ve missed the calls. That time is very awkward for me and I’ve
occasionally been confused by Wednesday/Thursday switches.

 

Regards,

Eric

 

 

________________________________

From: Jones, Andy [mailto:And...@li...] 
Sent: Friday, November 21, 2008 2:09 AM
To: Eric Deutsch
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Eric,

 

Would you be able to do a couple of updates to the auto-generated docs? There’s
a couple of errors to fix.

 

When there is an instance of: <xsd:element ref="pf:DatabaseReference"
minOccurs="0">, would you be able to retrieve the documentation in the table
from the referenced element.

 

Also, when an element is inherited from, documentation for inherited attributes
does not appear in the table (e.g. see Specificity rule, no docs for cvRef,
unitName etc.) – unless we were missing documentation for these attributes when
it was last generated?.

 

There are also a few instances of elements imported from the FuGE-light schema
which are completely empty, no attributes or documentation e.g. Organization or
Person.

 

We’re aiming to submit the specs to the PSI process by the end of month (i.e. a
week on Monday), so if you would be able to look at this fairly soon it would be
very much appreciated! Also, any chance that you can get someone to generate the
TPP and SpectraST examples at your end. It’s no disaster if we submit to the
process without these but it would be beneficial.

 

Cheers

Andy

 

 

 

 

 

 

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: 17 October 2008 07:43
To: psi...@li...
Subject: Re: [Psidev-pi-dev] Spec doc

 

Hi everyone, I updated the current draft of the on-line autogenerated schema
docs to the latest svn. The result is at:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working.html

 

It looks like the current mapping file is just a template without any term
mappings themselves. Just as a test, I wrote into the axml-mapping.xml file the
mapping information for SearchType and it seemed to pull it out of the CV
nicely:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working.html#SearchType

 

The autogeneration pulls examples out of one file. I randomly chose
Mascot_MSMS_example.axml. Is there a better instance document to automatically
pull examples out of?

 

Regards,

Eric

 

 

 

________________________________

From: Jones, Andy [mailto:And...@li...] 
Sent: Monday, October 13, 2008 7:07 AM
To: psi...@li...
Subject: [Psidev-pi-dev] Spec doc

 

Hi all,

 

A new version of the spec document has been uploaded by SVN (in the
specification_document directory), and previous versions have been put in a
subfolder. I think the document is getting there... 

 

Main tasks still to do:

 

Finish section on use cases when we have finally agreed the list online and made
all the example files.

Import some parts of the example files to demonstrate a few specific points

Import the autogenerated documentation

 

Before we can submit, the main outstanding issues are:

 

CV - looking through the CV there is still a fair bit of work to do, there’s
quite a few terms with missing or incorrect documentation

Mapping file

Finish example files.

 

Prior to the call on Thurs, can we have a think about how we plan to get the CV
into shape and discuss it as a main agenda item...

 

Also new schema uploaded with a few bits of improved documentation.

Cheers

Andy

 

 

 

 

 

 

 

 

 

 

 

 

 

 
 


________________________________



 
 
 
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
 
 


________________________________



 
 
 
_______________________________________________
Psidev-pi-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
  





-- 
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344
 
dc...@ma...
http://www.matrixscience.com
 
Matrix Science Ltd. is registered in England and Wales
Company number 3533898
 
 
 


________________________________



 
 
 
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Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
  

Re: [Psidev-pi-dev] FW: Spec doc

[Jones, A. <And...@li...>]

Hi all,

 

New schema uploaded:

 

Various documentation changes, as discussed below.

 

PlusValue / MinusValue now encoded as CVParams

 

Made a change to AnalysisProtocolCollection and AnalysisCollection that
prevented GenericProtocol and GenericProtocolApplication being used – I’ve been
meaning to fix this for a while. It also means the files are now restricted to
containing at most one ProteinDetection and one ProteinDetectionApplication.

 

In the schema, we have some fairly pointless abstract classes AnalysisProtocol
and AnalysisProtocolApplication. They were put in the schema at one stage to
demonstrate how the format should be extended in the future, following this
design pattern (or something like this...). I vote we get rid of them, and write
in the spec document about future extension strategies.

 

Cheers

Andy

 

 

 

 

 

 

 

 

From: Jones, Andy [mailto:And...@li...] 
Sent: 02 December 2008 12:23
To: psi...@li...
Subject: Re: [Psidev-pi-dev] FW: Spec doc

 

Hi David,

 

The changes relating the instance docs are coming from the Mascot MS/MS example
so these are for you to fix ;-)

 

Eric, are you able to import certain parts of the instance docs from other
examples. Element <DatabaseTranslation> could take examples from
Mascot_NA_example.axml? 

 

I’ll make the other recommended changes to the XSD documentation (some of these
require a fix to the generating script, which I’ve flagged to Eric separately).

 

Martin, are you happy for us to make the change relating to peptide mass
documentation (see below).

 

>semiSpecific - shouldn't this be a boolean?

 

Agreed, I’ll make this change.

 

><PlusValue>

 

Eric is right to query this part of the schema. In fact, we’ve used the
PropertyValue element only for PlusValue and MinusValue in the entire schema.
Let’s make these CV terms:

 

<pf:cvParam accession="PI:00999" name="search tolerance plus value" value=”0.5”
cvRef="PSI-PI"

unitAccession="UO:0000221" name="dalton" cvRef="UO" />

 

Andreas can you add: “search tolerance plus value” and “search tolerance minus
value” to the CV and mapping file and I’ll change the schema, does this seem
reasonable to everyone…?

 

Getting there…

 

Cheers

Andy

 

 

 

 

From: Pierre-Alain Binz [mailto:pie...@is...] 
Sent: 02 December 2008 11:17
To: David Creasy
Cc: psi...@li...
Subject: Re: [Psidev-pi-dev] FW: Spec doc

 

Hi,

David Creasy wrote: 

Hi Andy,

Some minor changes:

From:
<pf:Person id="PERSON_DOC_OWNER" firstName="" lastName="Some Person"
email="so...@so..." <mailto:so...@so...> >
to:
<pf:Person id="PERSON_DOC_OWNER" firstName="Some" lastName="Person"
email="so...@so..." <mailto:so...@so...> >
 
 
Example Context:      
<pf:cv id="PSI-PI"        fullName="PSI-PI"        URI=MailScanner has detected
a possible fraud attempt from "www.psidev.info" claiming to be
"http://www.psidev.info/not_sure_of_url_to_cv.obo"
<http://www.psidev.info/not_sure_of_url_to_cv.obo> ></pf:cv>
We only want the cv psidev.info when we finally release. Guess it's OK to leave
this as it is at the moment.
 
 
Element <AnalysisSoftware>
Definition:   A data set containing spectra data (consisting of one or more
spectra). 
Definition looks like a copy and paste of something quite different!
 
 
Element <pf:ContactRole>
Definition:   The Contact that provided the document instance. 
We use the contact role in several different places. Definition needs to be a
bit more general? 
In the example it is for a software vendor.
 
 
 
Element <pf:Person>
Example needs filling out a bit with some fictitious person.
 
 
Element <Peptide>
sequenceMass xsd:double - The sum of the unmodified (poly)peptide sequence
residues, exclusive of the termini masses in Daltons.
  

Oh dear. Some of the examples are inclusive of the termini masses and any
modifications, others are not. In theory, it's possible to calculate the mass
given the modification delta and the CTermGain="OH" NTermGain="H" from the
enzyme. However, that's not trivial in a case of multiple enzymes. I'd suggest
we change the definition to include the termini and mods. Martin (whose examples
followed the documentation)  may think differently?

I aggree: with termini and mods. Calculated neutral mass in Da (not m/z),
monoisotopic, 6digits after unit?



Element <Inputs>
Definition:     The inputs to the analyses including the databases searched and
the spectral data 
The example shows the input file to the process that created the analysisXML
document (the Mascot .dat file)
The global definition needs changing. Also, need to add a definition for
SpectraData.


Element <DatabaseTranslation>
Could take examples from Mascot_NA_example.axml


Element <Enzyme>
missedCleavages    xsd:int    optional    URI of the analysis software e.g.
manufacturer's website
semiSpecific - shouldn't this be a boolean?


Element <PlusValue>
unitName    xsd:string    -    The name of the unit.
Shame that it doesn't pull out the allowed CV from the mapping file:

<CvTerm termAccession="UO:0000221" useTermName="false" useTerm="true"
termName="dalton" cvIdentifierRef="UO" />
<CvTerm termAccession="UO:0000166" useTermName="false" useTerm="false"
termName="parts per notation" cvIdentifierRef="UO" />

Element <SpectrumIdentificationItem>
Has an attribute of rank and also a CV item. From the minutes here:
http://psidev.info/index.php?q=node/380
Looks as though we agreed it should be an attribute and removed from the CV

Cheers,
David

Jones, Andy wrote: 

Hi all,

Eric has re-generated the schema documentation for us. This is getting fairly
close to a version I can cut and paste into the spec doc. Let me know if you
have any comments,

Cheers

Andy

 

 

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: 01 December 2008 09:23
To: Jones, Andy
Cc: 'Eric Deutsch'
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Andy, sorry for the delay, US holiday over here. You will find updated HTML
documentation at:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working.html

 

A version that is suitable for cut-n-paste into a word doc is at:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working_simple.html

 

I fixed some of the problems. The main problem I still know about is that in the
subelement listing, any subelements that are double-tall nested substitution
grouped elements do not have their definition visible. If one clicks on the
subelement, the main element does have a definition. So it’s there, but my
program is stymied by the various levels. This is fixable, but probably not
before submission.

 

If you send me screen-capture images to embed in some elements, that can be done
if you like.

 

If there are still other outstanding issues, please let me know

 

Regards,

Eric

 

 

 

 

________________________________

From: Jones, Andy [mailto:And...@li...] 
Sent: Thursday, November 27, 2008 4:56 AM
To: Eric Deutsch
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Eric,

 

Any chance you could look at the generated documentation this week? We’re aiming
to submit the specs to the document process by Monday...

Thanks

Andy

 

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: 21 November 2008 17:44
To: Jones, Andy
Cc: 'Eric Deutsch'
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Andy, yes, I will fix the bugs and regenerate the docs from the latest schema
and files early next week.

 

I will also have a look at TPP related materials for AnalysisXML and get back to
you.

 

Sorry I’ve missed the calls. That time is very awkward for me and I’ve
occasionally been confused by Wednesday/Thursday switches.

 

Regards,

Eric

 

 

________________________________

From: Jones, Andy [mailto:And...@li...] 
Sent: Friday, November 21, 2008 2:09 AM
To: Eric Deutsch
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Eric,

 

Would you be able to do a couple of updates to the auto-generated docs? There’s
a couple of errors to fix.

 

When there is an instance of: <xsd:element ref="pf:DatabaseReference"
minOccurs="0">, would you be able to retrieve the documentation in the table
from the referenced element.

 

Also, when an element is inherited from, documentation for inherited attributes
does not appear in the table (e.g. see Specificity rule, no docs for cvRef,
unitName etc.) – unless we were missing documentation for these attributes when
it was last generated?.

 

There are also a few instances of elements imported from the FuGE-light schema
which are completely empty, no attributes or documentation e.g. Organization or
Person.

 

We’re aiming to submit the specs to the PSI process by the end of month (i.e. a
week on Monday), so if you would be able to look at this fairly soon it would be
very much appreciated! Also, any chance that you can get someone to generate the
TPP and SpectraST examples at your end. It’s no disaster if we submit to the
process without these but it would be beneficial.

 

Cheers

Andy

 

 

 

 

 

 

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: 17 October 2008 07:43
To: psi...@li...
Subject: Re: [Psidev-pi-dev] Spec doc

 

Hi everyone, I updated the current draft of the on-line autogenerated schema
docs to the latest svn. The result is at:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working.html

 

It looks like the current mapping file is just a template without any term
mappings themselves. Just as a test, I wrote into the axml-mapping.xml file the
mapping information for SearchType and it seemed to pull it out of the CV
nicely:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working.html#SearchType

 

The autogeneration pulls examples out of one file. I randomly chose
Mascot_MSMS_example.axml. Is there a better instance document to automatically
pull examples out of?

 

Regards,

Eric

 

 

 

________________________________

From: Jones, Andy [mailto:And...@li...] 
Sent: Monday, October 13, 2008 7:07 AM
To: psi...@li...
Subject: [Psidev-pi-dev] Spec doc

 

Hi all,

 

A new version of the spec document has been uploaded by SVN (in the
specification_document directory), and previous versions have been put in a
subfolder. I think the document is getting there... 

 

Main tasks still to do:

 

Finish section on use cases when we have finally agreed the list online and made
all the example files.

Import some parts of the example files to demonstrate a few specific points

Import the autogenerated documentation

 

Before we can submit, the main outstanding issues are:

 

CV - looking through the CV there is still a fair bit of work to do, there’s
quite a few terms with missing or incorrect documentation

Mapping file

Finish example files.

 

Prior to the call on Thurs, can we have a think about how we plan to get the CV
into shape and discuss it as a main agenda item...

 

Also new schema uploaded with a few bits of improved documentation.

Cheers

Andy

 

 

 

 

 

 

 

 

 

 

 

 

 

 
 
 
 


________________________________



 
 
 
 
 
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
 
 
 
 


________________________________



 
 
 
 
 
_______________________________________________
Psidev-pi-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
  

 

-- 
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344
 
dc...@ma...
http://www.matrixscience.com
 
Matrix Science Ltd. is registered in England and Wales
Company number 3533898
 
 
 
 
 


________________________________



 
 
 
 
 
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
 
 
 
 
 


________________________________



 
 
 
 
 
_______________________________________________
Psidev-pi-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
  

Re: [Psidev-pi-dev] FW: Spec doc

[Jones, A. <And...@li...>]

Hi all,

 

I’ve uploaded a new version of the spec doc, in which I’ve inserted the
auto-generated documentation. There’s still a few things to fix with this (the
schema updates from yesterday have not been incorporated yet) but at this stage
it would be really useful if everyone could take a look and provide feedback
(http://code.google.com/p/psi-pi/source/browse/#svn/trunk/specification_document
).

 

Main questions:

 

-          Are we generally happy with this format?

-          Are there any major omissions?

 

I think we all agree that we want to the this submitted ASAP to the PSI document
process, so if you could get feedback to me this week it would be much
appreciated,

Cheers

Andy

 

 

 

 

From: Jones, Andy [mailto:And...@li...] 
Sent: 02 December 2008 17:36
To: psi...@li...
Subject: Re: [Psidev-pi-dev] FW: Spec doc

 

Hi all,

 

New schema uploaded:

 

Various documentation changes, as discussed below.

 

PlusValue / MinusValue now encoded as CVParams

 

Made a change to AnalysisProtocolCollection and AnalysisCollection that
prevented GenericProtocol and GenericProtocolApplication being used – I’ve been
meaning to fix this for a while. It also means the files are now restricted to
containing at most one ProteinDetection and one ProteinDetectionApplication.

 

In the schema, we have some fairly pointless abstract classes AnalysisProtocol
and AnalysisProtocolApplication. They were put in the schema at one stage to
demonstrate how the format should be extended in the future, following this
design pattern (or something like this...). I vote we get rid of them, and write
in the spec document about future extension strategies.

 

Cheers

Andy

 

 

 

 

 

 

 

 

From: Jones, Andy [mailto:And...@li...] 
Sent: 02 December 2008 12:23
To: psi...@li...
Subject: Re: [Psidev-pi-dev] FW: Spec doc

 

Hi David,

 

The changes relating the instance docs are coming from the Mascot MS/MS example
so these are for you to fix ;-)

 

Eric, are you able to import certain parts of the instance docs from other
examples. Element <DatabaseTranslation> could take examples from
Mascot_NA_example.axml? 

 

I’ll make the other recommended changes to the XSD documentation (some of these
require a fix to the generating script, which I’ve flagged to Eric separately).

 

Martin, are you happy for us to make the change relating to peptide mass
documentation (see below).

 

>semiSpecific - shouldn't this be a boolean?

 

Agreed, I’ll make this change.

 

><PlusValue>

 

Eric is right to query this part of the schema. In fact, we’ve used the
PropertyValue element only for PlusValue and MinusValue in the entire schema.
Let’s make these CV terms:

 

<pf:cvParam accession="PI:00999" name="search tolerance plus value" value=”0.5”
cvRef="PSI-PI"

unitAccession="UO:0000221" name="dalton" cvRef="UO" />

 

Andreas can you add: “search tolerance plus value” and “search tolerance minus
value” to the CV and mapping file and I’ll change the schema, does this seem
reasonable to everyone…?

 

Getting there…

 

Cheers

Andy

 

 

 

 

From: Pierre-Alain Binz [mailto:pie...@is...] 
Sent: 02 December 2008 11:17
To: David Creasy
Cc: psi...@li...
Subject: Re: [Psidev-pi-dev] FW: Spec doc

 

Hi,

David Creasy wrote: 

Hi Andy,

Some minor changes:

From:
<pf:Person id="PERSON_DOC_OWNER" firstName="" lastName="Some Person"
email="so...@so..." <mailto:so...@so...> >
to:
<pf:Person id="PERSON_DOC_OWNER" firstName="Some" lastName="Person"
email="so...@so..." <mailto:so...@so...> >
 
 
Example Context:      
<pf:cv id="PSI-PI"        fullName="PSI-PI"        URI=MailScanner has detected
a possible fraud attempt from "www.psidev.info" claiming to be
"http://www.psidev.info/not_sure_of_url_to_cv.obo"
<http://www.psidev.info/not_sure_of_url_to_cv.obo> ></pf:cv>
We only want the cv psidev.info when we finally release. Guess it's OK to leave
this as it is at the moment.
 
 
Element <AnalysisSoftware>
Definition:   A data set containing spectra data (consisting of one or more
spectra). 
Definition looks like a copy and paste of something quite different!
 
 
Element <pf:ContactRole>
Definition:   The Contact that provided the document instance. 
We use the contact role in several different places. Definition needs to be a
bit more general? 
In the example it is for a software vendor.
 
 
 
Element <pf:Person>
Example needs filling out a bit with some fictitious person.
 
 
Element <Peptide>
sequenceMass xsd:double - The sum of the unmodified (poly)peptide sequence
residues, exclusive of the termini masses in Daltons.
  

Oh dear. Some of the examples are inclusive of the termini masses and any
modifications, others are not. In theory, it's possible to calculate the mass
given the modification delta and the CTermGain="OH" NTermGain="H" from the
enzyme. However, that's not trivial in a case of multiple enzymes. I'd suggest
we change the definition to include the termini and mods. Martin (whose examples
followed the documentation)  may think differently?

I aggree: with termini and mods. Calculated neutral mass in Da (not m/z),
monoisotopic, 6digits after unit?



Element <Inputs>
Definition:     The inputs to the analyses including the databases searched and
the spectral data 
The example shows the input file to the process that created the analysisXML
document (the Mascot .dat file)
The global definition needs changing. Also, need to add a definition for
SpectraData.


Element <DatabaseTranslation>
Could take examples from Mascot_NA_example.axml


Element <Enzyme>
missedCleavages    xsd:int    optional    URI of the analysis software e.g.
manufacturer's website
semiSpecific - shouldn't this be a boolean?


Element <PlusValue>
unitName    xsd:string    -    The name of the unit.
Shame that it doesn't pull out the allowed CV from the mapping file:

<CvTerm termAccession="UO:0000221" useTermName="false" useTerm="true"
termName="dalton" cvIdentifierRef="UO" />
<CvTerm termAccession="UO:0000166" useTermName="false" useTerm="false"
termName="parts per notation" cvIdentifierRef="UO" />

Element <SpectrumIdentificationItem>
Has an attribute of rank and also a CV item. From the minutes here:
http://psidev.info/index.php?q=node/380
Looks as though we agreed it should be an attribute and removed from the CV

Cheers,
David

Jones, Andy wrote: 

Hi all,

Eric has re-generated the schema documentation for us. This is getting fairly
close to a version I can cut and paste into the spec doc. Let me know if you
have any comments,

Cheers

Andy

 

 

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: 01 December 2008 09:23
To: Jones, Andy
Cc: 'Eric Deutsch'
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Andy, sorry for the delay, US holiday over here. You will find updated HTML
documentation at:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working.html

 

A version that is suitable for cut-n-paste into a word doc is at:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working_simple.html

 

I fixed some of the problems. The main problem I still know about is that in the
subelement listing, any subelements that are double-tall nested substitution
grouped elements do not have their definition visible. If one clicks on the
subelement, the main element does have a definition. So it’s there, but my
program is stymied by the various levels. This is fixable, but probably not
before submission.

 

If you send me screen-capture images to embed in some elements, that can be done
if you like.

 

If there are still other outstanding issues, please let me know

 

Regards,

Eric

 

 

 

 

________________________________

From: Jones, Andy [mailto:And...@li...] 
Sent: Thursday, November 27, 2008 4:56 AM
To: Eric Deutsch
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Eric,

 

Any chance you could look at the generated documentation this week? We’re aiming
to submit the specs to the document process by Monday...

Thanks

Andy

 

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: 21 November 2008 17:44
To: Jones, Andy
Cc: 'Eric Deutsch'
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Andy, yes, I will fix the bugs and regenerate the docs from the latest schema
and files early next week.

 

I will also have a look at TPP related materials for AnalysisXML and get back to
you.

 

Sorry I’ve missed the calls. That time is very awkward for me and I’ve
occasionally been confused by Wednesday/Thursday switches.

 

Regards,

Eric

 

 

________________________________

From: Jones, Andy [mailto:And...@li...] 
Sent: Friday, November 21, 2008 2:09 AM
To: Eric Deutsch
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Eric,

 

Would you be able to do a couple of updates to the auto-generated docs? There’s
a couple of errors to fix.

 

When there is an instance of: <xsd:element ref="pf:DatabaseReference"
minOccurs="0">, would you be able to retrieve the documentation in the table
from the referenced element.

 

Also, when an element is inherited from, documentation for inherited attributes
does not appear in the table (e.g. see Specificity rule, no docs for cvRef,
unitName etc.) – unless we were missing documentation for these attributes when
it was last generated?.

 

There are also a few instances of elements imported from the FuGE-light schema
which are completely empty, no attributes or documentation e.g. Organization or
Person.

 

We’re aiming to submit the specs to the PSI process by the end of month (i.e. a
week on Monday), so if you would be able to look at this fairly soon it would be
very much appreciated! Also, any chance that you can get someone to generate the
TPP and SpectraST examples at your end. It’s no disaster if we submit to the
process without these but it would be beneficial.

 

Cheers

Andy

 

 

 

 

 

 

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: 17 October 2008 07:43
To: psi...@li...
Subject: Re: [Psidev-pi-dev] Spec doc

 

Hi everyone, I updated the current draft of the on-line autogenerated schema
docs to the latest svn. The result is at:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working.html

 

It looks like the current mapping file is just a template without any term
mappings themselves. Just as a test, I wrote into the axml-mapping.xml file the
mapping information for SearchType and it seemed to pull it out of the CV
nicely:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working.html#SearchType

 

The autogeneration pulls examples out of one file. I randomly chose
Mascot_MSMS_example.axml. Is there a better instance document to automatically
pull examples out of?

 

Regards,

Eric

 

 

 

________________________________

From: Jones, Andy [mailto:And...@li...] 
Sent: Monday, October 13, 2008 7:07 AM
To: psi...@li...
Subject: [Psidev-pi-dev] Spec doc

 

Hi all,

 

A new version of the spec document has been uploaded by SVN (in the
specification_document directory), and previous versions have been put in a
subfolder. I think the document is getting there... 

 

Main tasks still to do:

 

Finish section on use cases when we have finally agreed the list online and made
all the example files.

Import some parts of the example files to demonstrate a few specific points

Import the autogenerated documentation

 

Before we can submit, the main outstanding issues are:

 

CV - looking through the CV there is still a fair bit of work to do, there’s
quite a few terms with missing or incorrect documentation

Mapping file

Finish example files.

 

Prior to the call on Thurs, can we have a think about how we plan to get the CV
into shape and discuss it as a main agenda item...

 

Also new schema uploaded with a few bits of improved documentation.

Cheers

Andy

 

 

 

 

 

 

 

 

 

 

 

 

 

 
 
 
 
 
 


________________________________



 
 
 
 
 
 
 
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
 
 
 
 
 
 


________________________________



 
 
 
 
 
 
 
_______________________________________________
Psidev-pi-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
  

 

-- 
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344
 
dc...@ma...
http://www.matrixscience.com
 
Matrix Science Ltd. is registered in England and Wales
Company number 3533898
 
 
 
 
 
 
 


________________________________



 
 
 
 
 
 
 
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
 
 
 
 
 
 
 


________________________________



 
 
 
 
 
 
 
_______________________________________________
Psidev-pi-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
  

Re: [Psidev-pi-dev] FW: Spec doc

[Jones, A. <And...@li...>]

Hi all,

 

Jenny has pointed out that the images are missing from the uploaded version,
they seem to be hyperlinked to images stored locally on my machine (which
happened during the conversion from html to word). If anyone knows how to get
around this problem (without manually inserting each image), let me know. 

Cheers

Andy

 

From: Jones, Andy [mailto:And...@li...] 
Sent: 03 December 2008 10:13
To: psi...@li...
Subject: Re: [Psidev-pi-dev] FW: Spec doc

 

Hi all,

 

I’ve uploaded a new version of the spec doc, in which I’ve inserted the
auto-generated documentation. There’s still a few things to fix with this (the
schema updates from yesterday have not been incorporated yet) but at this stage
it would be really useful if everyone could take a look and provide feedback
(http://code.google.com/p/psi-pi/source/browse/#svn/trunk/specification_document
).

 

Main questions:

 

-          Are we generally happy with this format?

-          Are there any major omissions?

 

I think we all agree that we want to the this submitted ASAP to the PSI document
process, so if you could get feedback to me this week it would be much
appreciated,

Cheers

Andy

 

 

 

 

From: Jones, Andy [mailto:And...@li...] 
Sent: 02 December 2008 17:36
To: psi...@li...
Subject: Re: [Psidev-pi-dev] FW: Spec doc

 

Hi all,

 

New schema uploaded:

 

Various documentation changes, as discussed below.

 

PlusValue / MinusValue now encoded as CVParams

 

Made a change to AnalysisProtocolCollection and AnalysisCollection that
prevented GenericProtocol and GenericProtocolApplication being used – I’ve been
meaning to fix this for a while. It also means the files are now restricted to
containing at most one ProteinDetection and one ProteinDetectionApplication.

 

In the schema, we have some fairly pointless abstract classes AnalysisProtocol
and AnalysisProtocolApplication. They were put in the schema at one stage to
demonstrate how the format should be extended in the future, following this
design pattern (or something like this...). I vote we get rid of them, and write
in the spec document about future extension strategies.

 

Cheers

Andy

 

 

 

 

 

 

 

 

From: Jones, Andy [mailto:And...@li...] 
Sent: 02 December 2008 12:23
To: psi...@li...
Subject: Re: [Psidev-pi-dev] FW: Spec doc

 

Hi David,

 

The changes relating the instance docs are coming from the Mascot MS/MS example
so these are for you to fix ;-)

 

Eric, are you able to import certain parts of the instance docs from other
examples. Element <DatabaseTranslation> could take examples from
Mascot_NA_example.axml? 

 

I’ll make the other recommended changes to the XSD documentation (some of these
require a fix to the generating script, which I’ve flagged to Eric separately).

 

Martin, are you happy for us to make the change relating to peptide mass
documentation (see below).

 

>semiSpecific - shouldn't this be a boolean?

 

Agreed, I’ll make this change.

 

><PlusValue>

 

Eric is right to query this part of the schema. In fact, we’ve used the
PropertyValue element only for PlusValue and MinusValue in the entire schema.
Let’s make these CV terms:

 

<pf:cvParam accession="PI:00999" name="search tolerance plus value" value=”0.5”
cvRef="PSI-PI"

unitAccession="UO:0000221" name="dalton" cvRef="UO" />

 

Andreas can you add: “search tolerance plus value” and “search tolerance minus
value” to the CV and mapping file and I’ll change the schema, does this seem
reasonable to everyone…?

 

Getting there…

 

Cheers

Andy

 

 

 

 

From: Pierre-Alain Binz [mailto:pie...@is...] 
Sent: 02 December 2008 11:17
To: David Creasy
Cc: psi...@li...
Subject: Re: [Psidev-pi-dev] FW: Spec doc

 

Hi,

David Creasy wrote: 

Hi Andy,

Some minor changes:

From:
<pf:Person id="PERSON_DOC_OWNER" firstName="" lastName="Some Person"
email="so...@so..." <mailto:so...@so...> >
to:
<pf:Person id="PERSON_DOC_OWNER" firstName="Some" lastName="Person"
email="so...@so..." <mailto:so...@so...> >
 
 
Example Context:      
<pf:cv id="PSI-PI"        fullName="PSI-PI"        URI=MailScanner has detected
a possible fraud attempt from "www.psidev.info" claiming to be
"http://www.psidev.info/not_sure_of_url_to_cv.obo"
<http://www.psidev.info/not_sure_of_url_to_cv.obo> ></pf:cv>
We only want the cv psidev.info when we finally release. Guess it's OK to leave
this as it is at the moment.
 
 
Element <AnalysisSoftware>
Definition:   A data set containing spectra data (consisting of one or more
spectra). 
Definition looks like a copy and paste of something quite different!
 
 
Element <pf:ContactRole>
Definition:   The Contact that provided the document instance. 
We use the contact role in several different places. Definition needs to be a
bit more general? 
In the example it is for a software vendor.
 
 
 
Element <pf:Person>
Example needs filling out a bit with some fictitious person.
 
 
Element <Peptide>
sequenceMass xsd:double - The sum of the unmodified (poly)peptide sequence
residues, exclusive of the termini masses in Daltons.
  

Oh dear. Some of the examples are inclusive of the termini masses and any
modifications, others are not. In theory, it's possible to calculate the mass
given the modification delta and the CTermGain="OH" NTermGain="H" from the
enzyme. However, that's not trivial in a case of multiple enzymes. I'd suggest
we change the definition to include the termini and mods. Martin (whose examples
followed the documentation)  may think differently?

I aggree: with termini and mods. Calculated neutral mass in Da (not m/z),
monoisotopic, 6digits after unit?



Element <Inputs>
Definition:     The inputs to the analyses including the databases searched and
the spectral data 
The example shows the input file to the process that created the analysisXML
document (the Mascot .dat file)
The global definition needs changing. Also, need to add a definition for
SpectraData.


Element <DatabaseTranslation>
Could take examples from Mascot_NA_example.axml


Element <Enzyme>
missedCleavages    xsd:int    optional    URI of the analysis software e.g.
manufacturer's website
semiSpecific - shouldn't this be a boolean?


Element <PlusValue>
unitName    xsd:string    -    The name of the unit.
Shame that it doesn't pull out the allowed CV from the mapping file:

<CvTerm termAccession="UO:0000221" useTermName="false" useTerm="true"
termName="dalton" cvIdentifierRef="UO" />
<CvTerm termAccession="UO:0000166" useTermName="false" useTerm="false"
termName="parts per notation" cvIdentifierRef="UO" />

Element <SpectrumIdentificationItem>
Has an attribute of rank and also a CV item. From the minutes here:
http://psidev.info/index.php?q=node/380
Looks as though we agreed it should be an attribute and removed from the CV

Cheers,
David

Jones, Andy wrote: 

Hi all,

Eric has re-generated the schema documentation for us. This is getting fairly
close to a version I can cut and paste into the spec doc. Let me know if you
have any comments,

Cheers

Andy

 

 

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: 01 December 2008 09:23
To: Jones, Andy
Cc: 'Eric Deutsch'
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Andy, sorry for the delay, US holiday over here. You will find updated HTML
documentation at:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working.html

 

A version that is suitable for cut-n-paste into a word doc is at:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working_simple.html

 

I fixed some of the problems. The main problem I still know about is that in the
subelement listing, any subelements that are double-tall nested substitution
grouped elements do not have their definition visible. If one clicks on the
subelement, the main element does have a definition. So it’s there, but my
program is stymied by the various levels. This is fixable, but probably not
before submission.

 

If you send me screen-capture images to embed in some elements, that can be done
if you like.

 

If there are still other outstanding issues, please let me know

 

Regards,

Eric

 

 

 

 

________________________________

From: Jones, Andy [mailto:And...@li...] 
Sent: Thursday, November 27, 2008 4:56 AM
To: Eric Deutsch
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Eric,

 

Any chance you could look at the generated documentation this week? We’re aiming
to submit the specs to the document process by Monday...

Thanks

Andy

 

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: 21 November 2008 17:44
To: Jones, Andy
Cc: 'Eric Deutsch'
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Andy, yes, I will fix the bugs and regenerate the docs from the latest schema
and files early next week.

 

I will also have a look at TPP related materials for AnalysisXML and get back to
you.

 

Sorry I’ve missed the calls. That time is very awkward for me and I’ve
occasionally been confused by Wednesday/Thursday switches.

 

Regards,

Eric

 

 

________________________________

From: Jones, Andy [mailto:And...@li...] 
Sent: Friday, November 21, 2008 2:09 AM
To: Eric Deutsch
Subject: RE: [Psidev-pi-dev] Spec doc

 

Hi Eric,

 

Would you be able to do a couple of updates to the auto-generated docs? There’s
a couple of errors to fix.

 

When there is an instance of: <xsd:element ref="pf:DatabaseReference"
minOccurs="0">, would you be able to retrieve the documentation in the table
from the referenced element.

 

Also, when an element is inherited from, documentation for inherited attributes
does not appear in the table (e.g. see Specificity rule, no docs for cvRef,
unitName etc.) – unless we were missing documentation for these attributes when
it was last generated?.

 

There are also a few instances of elements imported from the FuGE-light schema
which are completely empty, no attributes or documentation e.g. Organization or
Person.

 

We’re aiming to submit the specs to the PSI process by the end of month (i.e. a
week on Monday), so if you would be able to look at this fairly soon it would be
very much appreciated! Also, any chance that you can get someone to generate the
TPP and SpectraST examples at your end. It’s no disaster if we submit to the
process without these but it would be beneficial.

 

Cheers

Andy

 

 

 

 

 

 

From: Eric Deutsch [mailto:ede...@sy...] 
Sent: 17 October 2008 07:43
To: psi...@li...
Subject: Re: [Psidev-pi-dev] Spec doc

 

Hi everyone, I updated the current draft of the on-line autogenerated schema
docs to the latest svn. The result is at:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working.html

 

It looks like the current mapping file is just a template without any term
mappings themselves. Just as a test, I wrote into the axml-mapping.xml file the
mapping information for SearchType and it seemed to pull it out of the CV
nicely:

 

http://www.peptideatlas.org/tmp/AnalysisXML_working.html#SearchType

 

The autogeneration pulls examples out of one file. I randomly chose
Mascot_MSMS_example.axml. Is there a better instance document to automatically
pull examples out of?

 

Regards,

Eric

 

 

 

________________________________

From: Jones, Andy [mailto:And...@li...] 
Sent: Monday, October 13, 2008 7:07 AM
To: psi...@li...
Subject: [Psidev-pi-dev] Spec doc

 

Hi all,

 

A new version of the spec document has been uploaded by SVN (in the
specification_document directory), and previous versions have been put in a
subfolder. I think the document is getting there... 

 

Main tasks still to do:

 

Finish section on use cases when we have finally agreed the list online and made
all the example files.

Import some parts of the example files to demonstrate a few specific points

Import the autogenerated documentation

 

Before we can submit, the main outstanding issues are:

 

CV - looking through the CV there is still a fair bit of work to do, there’s
quite a few terms with missing or incorrect documentation

Mapping file

Finish example files.

 

Prior to the call on Thurs, can we have a think about how we plan to get the CV
into shape and discuss it as a main agenda item...

 

Also new schema uploaded with a few bits of improved documentation.

Cheers

Andy

 

 

 

 

 

 

 

 

 

 

 

 

 

 
 
 
 
 
 
 
 


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Re: [Psidev-pi-dev] FW: Spec doc

[David C. <dc...@ma...>]

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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Hi Andy, Andreas,<br>
<br>
I assume that this is a typo below:<br>
<pre><span style="font-size: 8pt;" lang="EN-US">&lt;pf:cvParam accession="PI:00999" name="search tolerance plus value" value=”0.5” cvRef="PSI-PI"<o:p></o:p></span></pre>
<p class="MsoNormal"><span
 style="font-size: 8pt; font-family: &quot;Courier New&quot;;" lang="EN-US">unitAccession="UO:0000221"
name="dalton" cvRef="UO" /&gt;<o:p></o:p></span></p>
<span style="color: rgb(31, 73, 125);"><o:p></o:p></span><br>
and the second cvRef is meant to be a unitCvRef??<br>
<br>
I've updated the Mascot_MSMS_example.axml, <br>
<small><tt>      &lt;FragmentTolerance&gt;<br>
        &lt;pf:cvParam accession="PI:00404" name="absolut mass unit"
value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton"
unitCvRef="UO" /&gt;<br>
        &lt;pf:cvParam accession="PI:00404" name="absolut mass unit"
value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton"
unitCvRef="UO" /&gt;<br>
      &lt;/FragmentTolerance&gt;<br>
      &lt;ParentTolerance&gt;<br>
        &lt;pf:cvParam accession="PI:00403" name="relative mass unit"
value="0.1" cvRef="PSI-PI" unitAccession="UO:0000187"
unitName="percent" unitCvRef="UO" /&gt;<br>
        &lt;pf:cvParam accession="PI:00403" name="relative mass unit"
value="0.1" cvRef="PSI-PI" unitAccession="UO:0000187"
unitName="percent" unitCvRef="UO" /&gt;<br>
      &lt;/ParentTolerance&gt;<br>
</tt></small><br>
<br>
but this doesn't validate:<br>
<br>
<pre><font color="red">Error: Unit CVTerm not allowed: UO:0000187 - percent of term PI:00403 - relative mass unit</font>
<font color="red">Error: Unit CVTerm not allowed: UO:0000221 - dalton of term PI:00404 - absolut mass unit</font>
<font color="red">Error: Value of CVTerm not allowed: 'PI:00403 - relative mass unit, value=0.1' at element '/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ParentTolerance'</font>
<font color="red">Error: Value of CVTerm not allowed: 'PI:00404 - absolut mass unit, value=0.5' at element '/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/FragmentTolerance'</font>
<font color="red">Error: Violated mapping rule 'R17a' number of term repeats at element '/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ParentTolerance'</font>
<font color="red">Error: Violated mapping rule 'R17b' number of term repeats at element '/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/FragmentTolerance'

</font></pre>
What am I doing wrong?<br>
<br>
I'm also slightly concerned about PSI-PI group getting the wrong(?)
reputation. Martin, could you change PI:00404 from being a brand of
vodka to "absolute". Thanks.<br>
(I've still not installed OboEdit.)<br>
<br>
David<br>
<br>
Jones, Andy wrote:
<blockquote
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  <div class="Section1">
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Hi all,<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">New
schema uploaded:<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Various
documentation changes, as
discussed below.<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">PlusValue
/ MinusValue now
encoded as CVParams<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Made a
change to
AnalysisProtocolCollection and AnalysisCollection that prevented
GenericProtocol and GenericProtocolApplication being used – I’ve been
meaning
to fix this for a while. It also means the files are now restricted to
containing at most one ProteinDetection and one
ProteinDetectionApplication.<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">In the
schema, we have some
fairly pointless abstract classes AnalysisProtocol and
AnalysisProtocolApplication. They were put in the schema at one stage
to
demonstrate how the format should be extended in the future, following
this
design pattern (or something like this...). I vote we get rid of them,
and
write in the spec document about future extension strategies.<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Cheers<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Andy<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <div
 style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
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  <div
 style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
  <p class="MsoNormal"><b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;; color: windowtext;"
 lang="EN-US">From:</span></b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;; color: windowtext;"
 lang="EN-US">
Jones, Andy [<a class="moz-txt-link-freetext" href="mailto:And...@li...">mailto:And...@li...</a>] <br>
  <b>Sent:</b> 02 December 2008 12:23<br>
  <b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a><br>
  <b>Subject:</b> Re: [Psidev-pi-dev] FW: Spec doc<o:p></o:p></span></p>
  </div>
  </div>
  <p class="MsoNormal"><o:p> </o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Hi David,<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">The
changes relating the
instance docs are coming from the Mascot MS/MS example so these are for
you to
fix ;-)<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Eric, are
you able to import
certain parts of the instance docs from other examples. Element
&lt;DatabaseTranslation&gt; could take examples from
Mascot_NA_example.axml? <o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">I’ll make
the other recommended
changes to the XSD documentation (some of these require a fix to the
generating
script, which I’ve flagged to Eric separately).<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Martin,
are you happy for us to
make the change relating to peptide mass documentation (see below).<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">&gt;semiSpecific
- shouldn't
this be a boolean?<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Agreed,
I’ll make this change.<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">&gt;&lt;PlusValue&gt;<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Eric is
right to query this part
of the schema. In fact, we’ve used the PropertyValue element only for
PlusValue
and MinusValue in the entire schema. Let’s make these CV terms:<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <pre><span style="font-size: 8pt;" lang="EN-US">&lt;pf:cvParam accession="PI:00999" name="search tolerance plus value" value=”0.5” cvRef="PSI-PI"<o:p></o:p></span></pre>
  <p class="MsoNormal"><span
 style="font-size: 8pt; font-family: &quot;Courier New&quot;;" lang="EN-US">unitAccession="UO:0000221"
name="dalton" cvRef="UO" /&gt;<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Andreas
can you add: “</span><span style="color: rgb(31, 73, 125);" lang="EN-US">search
tolerance plus value” and “search
tolerance minus value” to the CV and mapping file and I’ll change the
schema,
does this seem reasonable to everyone…?<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"
 lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"
 lang="EN-US">Getting there…<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"
 lang="EN-US"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"
 lang="EN-US">Cheers<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"
 lang="EN-US">Andy<o:p></o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
  <div
 style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
  <div>
  <div
 style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
  <p class="MsoNormal"><b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;; color: windowtext;"
 lang="EN-US">From:</span></b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;; color: windowtext;"
 lang="EN-US">
Pierre-Alain Binz [<a class="moz-txt-link-freetext" href="mailto:pie...@is...">mailto:pie...@is...</a>] <br>
  <b>Sent:</b> 02 December 2008 11:17<br>
  <b>To:</b> David Creasy<br>
  <b>Cc:</b> <a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a><br>
  <b>Subject:</b> Re: [Psidev-pi-dev] FW: Spec doc<o:p></o:p></span></p>
  </div>
  </div>
  <p class="MsoNormal"><o:p> </o:p></p>
  <p class="MsoNormal">Hi,<br>
  <br>
David Creasy wrote: <o:p></o:p></p>
  <p class="MsoNormal">Hi Andy,<br>
  <br>
Some minor changes:<o:p></o:p></p>
  <pre>From:<o:p></o:p></pre>
  <pre>&lt;pf:Person id="PERSON_DOC_OWNER" firstName="" lastName="Some Person" email=<a
 moz-do-not-send="true" href="mailto:so...@so...">"so...@so..."</a>&gt;<o:p></o:p></pre>
  <pre>to:<o:p></o:p></pre>
  <pre>&lt;pf:Person id="PERSON_DOC_OWNER" firstName="Some" lastName="Person" email=<a
 moz-do-not-send="true" href="mailto:so...@so...">"so...@so..."</a>&gt;<o:p></o:p></pre>
  <pre><o:p> </o:p></pre>
  <pre><o:p> </o:p></pre>
  <pre>Example Context:      <o:p></o:p></pre>
  <pre>&lt;pf:cv id="PSI-PI"        fullName="PSI-PI"        URI=<a
 moz-do-not-send="true"
 href="http://www.psidev.info/not_sure_of_url_to_cv.obo"><b><span
 style="color: red;">MailScanner has detected a possible fraud attempt from "www.psidev.info" claiming to be</span></b> "http://www.psidev.info/not_sure_of_url_to_cv.obo"</a>&gt;&lt;/pf:cv&gt;<o:p></o:p></pre>
  <pre>We only want the cv psidev.info when we finally release. Guess it's OK to leave this as it is at the moment.<o:p></o:p></pre>
  <pre><o:p> </o:p></pre>
  <pre><o:p> </o:p></pre>
  <pre>Element &lt;AnalysisSoftware&gt;<o:p></o:p></pre>
  <pre>Definition:   A data set containing spectra data (consisting of one or more spectra). <o:p></o:p></pre>
  <pre>Definition looks like a copy and paste of something quite different!<o:p></o:p></pre>
  <pre><o:p> </o:p></pre>
  <pre><o:p> </o:p></pre>
  <pre>Element &lt;pf:ContactRole&gt;<o:p></o:p></pre>
  <pre>Definition:   The Contact that provided the document instance. <o:p></o:p></pre>
  <pre>We use the contact role in several different places. Definition needs to be a bit more general? <o:p></o:p></pre>
  <pre>In the example it is for a software vendor.<o:p></o:p></pre>
  <pre><o:p> </o:p></pre>
  <pre><o:p> </o:p></pre>
  <pre><o:p> </o:p></pre>
  <pre>Element &lt;pf:Person&gt;<o:p></o:p></pre>
  <pre>Example needs filling out a bit with some fictitious person.<o:p></o:p></pre>
  <pre><o:p> </o:p></pre>
  <pre><o:p> </o:p></pre>
  <pre>Element &lt;Peptide&gt;<o:p></o:p></pre>
  <pre>sequenceMass xsd:double - The sum of the unmodified (poly)peptide sequence residues, exclusive of the termini masses in Daltons.<o:p></o:p></pre>
  <pre>  <o:p></o:p></pre>
  <p class="MsoNormal">Oh dear. Some of the examples are inclusive of
the termini
masses and any modifications, others are not. In theory, it's possible
to
calculate the mass given the modification delta and the
CTermGain="OH" NTermGain="H" from the enzyme. However,
that's not trivial in a case of multiple enzymes. I'd suggest we change
the
definition to include the termini and mods. Martin (whose examples
followed the
documentation)  may think differently?<o:p></o:p></p>
  <p class="MsoNormal" style="margin-bottom: 12pt;">I aggree: with
termini and
mods. Calculated neutral mass in Da (not m/z), monoisotopic, 6digits
after
unit?<o:p></o:p></p>
  <p class="MsoNormal"><br>
  <br>
Element &lt;Inputs&gt;<br>
Definition:     The inputs to the analyses including the
databases searched and the spectral data <br>
The example shows the input file to the process that created the
analysisXML
document (the Mascot .dat file)<br>
The global definition needs changing. Also, need to add a definition
for
SpectraData.<br>
  <br>
  <br>
Element &lt;DatabaseTranslation&gt;<br>
Could take examples from Mascot_NA_example.axml<br>
  <br>
  <br>
Element &lt;Enzyme&gt;<br>
missedCleavages    xsd:int   
optional    URI of the analysis software e.g. manufacturer's
website<br>
semiSpecific - shouldn't this be a boolean?<br>
  <br>
  <br>
Element &lt;PlusValue&gt;<br>
unitName    xsd:string    -    The
name of the unit.<br>
Shame that it doesn't pull out the allowed CV from the mapping file:<br>
  <br>
&lt;CvTerm termAccession="UO:0000221" useTermName="false"
useTerm="true" termName="dalton"
cvIdentifierRef="UO" /&gt;<br>
&lt;CvTerm termAccession="UO:0000166" useTermName="false"
useTerm="false" termName="parts per notation"
cvIdentifierRef="UO" /&gt;<br>
  <br>
Element &lt;SpectrumIdentificationItem&gt;<br>
Has an attribute of rank and also a CV item. From the minutes here:<br>
  <a moz-do-not-send="true"
 href="http://psidev.info/index.php?q=node/380">http://psidev.info/index.php?q=node/380</a><br>
Looks as though we agreed it should be an attribute and removed from
the CV<br>
  <br>
Cheers,<br>
David<br>
  <br>
Jones, Andy wrote: <o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Hi all,</span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Eric has
re-generated the schema
documentation for us. This is getting fairly close to a version I can
cut and
paste into the spec doc. Let me know if you have any comments,</span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Cheers</span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Andy</span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
  <div
 style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
  <div>
  <div
 style="border-style: solid none none; border-color: -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
  <p class="MsoNormal"><b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US">From:</span></b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"> Eric Deutsch [<a moz-do-not-send="true"
 href="mailto:ede...@sy...">mailto:ede...@sy...</a>]
  <br>
  <b>Sent:</b> 01 December 2008 09:23<br>
  <b>To:</b> Jones, Andy<br>
  <b>Cc:</b> 'Eric Deutsch'<br>
  <b>Subject:</b> RE: [Psidev-pi-dev] Spec doc</span><o:p></o:p></p>
  </div>
  </div>
  <p class="MsoNormal"> <o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US">Hi Andy, sorry for the delay, US holiday over here. You
will find
updated HTML documentation at:</span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span lang="EN-US"><a moz-do-not-send="true"
 href="http://www.peptideatlas.org/tmp/AnalysisXML_working.html">http://www.peptideatlas.org/tmp/AnalysisXML_working.html</a></span><o:p></o:p></p>
  <p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span lang="EN-US">A version that is suitable
for cut-n-paste
into a word doc is at:</span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span lang="EN-US"><a moz-do-not-send="true"
 href="http://www.peptideatlas.org/tmp/AnalysisXML_working_simple.html">http://www.peptideatlas.org/tmp/AnalysisXML_working_simple.html</a></span><o:p></o:p></p>
  <p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span lang="EN-US">I fixed some of the problems.
The main
problem I still know about is that in the subelement listing, any
subelements
that are double-tall nested substitution grouped elements do not have
their definition
visible. If one clicks on the subelement, the main element does have a
definition. So it’s there, but my program is stymied by the various
levels.
This is fixable, but probably not before submission.</span><o:p></o:p></p>
  <p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span lang="EN-US">If you send me screen-capture
images to embed
in some elements, that can be done if you like.</span><o:p></o:p></p>
  <p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span lang="EN-US">If there are still other
outstanding
issues, please let me know</span><o:p></o:p></p>
  <p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span lang="EN-US">Regards,</span><o:p></o:p></p>
  <p class="MsoNormal"><span lang="EN-US">Eric</span><o:p></o:p></p>
  <p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"> </span><o:p></o:p></p>
  <div
 style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
  <div>
  <div class="MsoNormal" style="text-align: center;" align="center"><span
 style="font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"
 lang="EN-US">
  <hr align="center" size="2" width="100%"></span></div>
  <p class="MsoNormal"><b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US">From:</span></b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"> Jones, Andy [<a moz-do-not-send="true"
 href="mailto:And...@li...">mailto:And...@li...</a>]
  <br>
  <b>Sent:</b> Thursday, November 27, 2008 4:56 AM<br>
  <b>To:</b> Eric Deutsch<br>
  <b>Subject:</b> RE: [Psidev-pi-dev] Spec doc</span><o:p></o:p></p>
  </div>
  <p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Hi Eric,</span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Any
chance you could look at the
generated documentation this week? We’re aiming to submit the specs to
the
document process by Monday...</span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Thanks</span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Andy</span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
  <div
 style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
  <div>
  <div
 style="border-style: solid none none; border-color: -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
  <p class="MsoNormal"><b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US">From:</span></b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"> Eric Deutsch [<a moz-do-not-send="true"
 href="mailto:ede...@sy...">mailto:ede...@sy...</a>]
  <br>
  <b>Sent:</b> 21 November 2008 17:44<br>
  <b>To:</b> Jones, Andy<br>
  <b>Cc:</b> 'Eric Deutsch'<br>
  <b>Subject:</b> RE: [Psidev-pi-dev] Spec doc</span><o:p></o:p></p>
  </div>
  </div>
  <p class="MsoNormal"> <o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US">Hi Andy, yes, I will fix the bugs and regenerate the docs
from the
latest schema and files early next week.</span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US">I will also have a look at TPP related materials for
AnalysisXML
and get back to you.</span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US">Sorry I’ve missed the calls. That time is very awkward
for me and
I’ve occasionally been confused by Wednesday/Thursday switches.</span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US">Regards,</span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US">Eric</span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"> </span><o:p></o:p></p>
  <div
 style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
  <div>
  <div class="MsoNormal" style="text-align: center;" align="center"><span
 style="font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"
 lang="EN-US">
  <hr align="center" size="2" width="100%"></span></div>
  <p class="MsoNormal"><b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US">From:</span></b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"> Jones, Andy [<a moz-do-not-send="true"
 href="mailto:And...@li...">mailto:And...@li...</a>]
  <br>
  <b>Sent:</b> Friday, November 21, 2008 2:09 AM<br>
  <b>To:</b> Eric Deutsch<br>
  <b>Subject:</b> RE: [Psidev-pi-dev] Spec doc</span><o:p></o:p></p>
  </div>
  <p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Hi Eric,</span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Would you
be able to do a couple
of updates to the auto-generated docs? There’s a couple of errors to
fix.</span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">When
there is an instance of:
&lt;xsd:element ref="pf:DatabaseReference" minOccurs="0"&gt;,
would you be able to retrieve the documentation in the table from the
referenced element.</span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Also,
when an element is
inherited from, documentation for inherited attributes does not appear
in the
table (e.g. see Specificity rule, no docs for cvRef, unitName etc.) –
unless we
were missing documentation for these attributes when it was last
generated?.</span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">There are
also a few instances
of elements imported from the FuGE-light schema which are completely
empty, no
attributes or documentation e.g. Organization or Person.</span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">We’re
aiming to submit the specs
to the PSI process by the end of month (i.e. a week on Monday), so if
you would
be able to look at this fairly soon it would be very much appreciated!
Also,
any chance that you can get someone to generate the TPP and SpectraST
examples
at your end. It’s no disaster if we submit to the process without these
but it
would be beneficial.</span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Cheers</span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Andy</span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
  <div
 style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
  <div>
  <div
 style="border-style: solid none none; border-color: -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
  <p class="MsoNormal"><b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US">From:</span></b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"> Eric Deutsch [<a moz-do-not-send="true"
 href="mailto:ede...@sy...">mailto:ede...@sy...</a>]
  <br>
  <b>Sent:</b> 17 October 2008 07:43<br>
  <b>To:</b> <a moz-do-not-send="true"
 href="mailto:psi...@li...">psi...@li...</a><br>
  <b>Subject:</b> Re: [Psidev-pi-dev] Spec doc</span><o:p></o:p></p>
  </div>
  </div>
  <p class="MsoNormal"> <o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US">Hi everyone, I updated the current draft of the on-line
autogenerated schema docs to the latest svn. The result is at:</span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"><a moz-do-not-send="true"
 href="http://www.peptideatlas.org/tmp/AnalysisXML_working.html">http://www.peptideatlas.org/tmp/AnalysisXML_working.html</a></span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;;"
 lang="EN-US">It
looks like the current mapping file is just a template without any term
mappings themselves. Just as a test, I wrote into the axml-mapping.xml
file the
mapping information for SearchType and it seemed to pull it out of the
CV
nicely:</span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"><a moz-do-not-send="true"
 href="http://www.peptideatlas.org/tmp/AnalysisXML_working.html#SearchType">http://www.peptideatlas.org/tmp/AnalysisXML_working.html#SearchType</a></span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;;"
 lang="EN-US">The
autogeneration pulls examples out of one file. I randomly chose
Mascot_MSMS_example.axml. Is there a better instance document to
automatically
pull examples out of?</span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;;"
 lang="EN-US">Regards,</span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;;"
 lang="EN-US">Eric</span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"> </span><o:p></o:p></p>
  <p class="MsoNormal"><span
 style="font-size: 10pt; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: navy;"
 lang="EN-US"> </span><o:p></o:p></p>
  <div
 style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
  <div>
  <div class="MsoNormal" style="text-align: center;" align="center"><span
 style="font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"
 lang="EN-US">
  <hr align="center" size="2" width="100%"></span></div>
  <p class="MsoNormal"><b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US">From:</span></b><span
 style="font-size: 10pt; font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;"
 lang="EN-US"> Jones, Andy [<a moz-do-not-send="true"
 href="mailto:And...@li...">mailto:And...@li...</a>]
  <br>
  <b>Sent:</b> Monday, October 13, 2008 7:07 AM<br>
  <b>To:</b> <a moz-do-not-send="true"
 href="mailto:psi...@li...">psi...@li...</a><br>
  <b>Subject:</b> [Psidev-pi-dev] Spec doc</span><o:p></o:p></p>
  </div>
  <p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
  <p class="MsoNormal">Hi all,<o:p></o:p></p>
  <p class="MsoNormal"> <o:p></o:p></p>
  <p class="MsoNormal">A new version of the spec document has been
uploaded by SVN
(in the specification_document directory), and previous versions have
been put
in a subfolder. I think the document is getting there... <o:p></o:p></p>
  <p class="MsoNormal"> <o:p></o:p></p>
  <p class="MsoNormal">Main tasks still to do:<o:p></o:p></p>
  <p class="MsoNormal"> <o:p></o:p></p>
  <p class="MsoListParagraph" style="text-indent: -18pt;">Finish
section on use
cases when we have finally agreed the list online and made all the
example
files.<o:p></o:p></p>
  <p class="MsoListParagraph" style="text-indent: -18pt;">Import some
parts of the
example files to demonstrate a few specific points<o:p></o:p></p>
  <p class="MsoListParagraph" style="text-indent: -18pt;">Import the
autogenerated
documentation<o:p></o:p></p>
  <p class="MsoNormal"> <o:p></o:p></p>
  <p class="MsoNormal">Before we can submit, the main outstanding
issues are:<o:p></o:p></p>
  <p class="MsoNormal"> <o:p></o:p></p>
  <p class="MsoListParagraph" style="text-indent: -18pt;">CV - looking
through the
CV there is still a fair bit of work to do, there’s quite a few terms
with
missing or incorrect documentation<o:p></o:p></p>
  <p class="MsoListParagraph" style="text-indent: -18pt;">Mapping file<o:p></o:p></p>
  <p class="MsoListParagraph" style="text-indent: -18pt;">Finish
example files.<o:p></o:p></p>
  <p class="MsoNormal"> <o:p></o:p></p>
  <p class="MsoNormal">Prior to the call on Thurs, can we have a think
about how we
plan to get the CV into shape and discuss it as a main agenda item...<o:p></o:p></p>
  <p class="MsoNormal"> <o:p></o:p></p>
  <p class="MsoNormal">Also new schema uploaded with a few bits of
improved
documentation.<o:p></o:p></p>
  <p class="MsoNormal">Cheers<o:p></o:p></p>
  <p class="MsoNormal">Andy<o:p></o:p></p>
  <p class="MsoNormal"> <o:p></o:p></p>
  <p class="MsoNormal"> <o:p></o:p></p>
  <p class="MsoNormal"> <o:p></o:p></p>
  <p class="MsoNormal"> <o:p></o:p></p>
  <p class="MsoNormal"> <o:p></o:p></p>
  <p class="MsoNormal" style="margin-left: 18pt;"> <o:p></o:p></p>
  <p class="MsoNormal"> <o:p></o:p></p>
  <p class="MsoNormal"> <o:p></o:p></p>
  <p class="MsoNormal"> <o:p></o:p></p>
  <p class="MsoNormal"> <o:p></o:p></p>
  <p class="MsoNormal"> <o:p></o:p></p>
  <p class="MsoNormal"> <o:p></o:p></p>
  <p class="MsoNormal"> <o:p></o:p></p>
  </div>
  </div>
  </div>
  </div>
  </div>
  </div>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;">
<hr align="center" size="4" width="90%">

  </pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre><o:p> </o:p></pre>
  <pre>-------------------------------------------------------------------------<o:p></o:p></pre>
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 href="http://moblin-contest.org/redirect.php?banner_id=100&amp;url=/">http://moblin-contest.org/redirect.php?banner_id=100&amp;url=/</a><o:p></o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;">
<hr align="center" size="4" width="90%">

  </pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre><o:p> </o:p></pre>
  <pre>_______________________________________________<o:p></o:p></pre>
  <pre>Psidev-pi-dev mailing list<o:p></o:p></pre>
  <pre><a moz-do-not-send="true"
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 href="https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev">https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev</a><o:p></o:p></pre>
  <pre>  <o:p></o:p></pre>
  <p class="MsoNormal" style="margin-bottom: 12pt;"><span
 style="font-size: 12pt; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"><o:p> </o:p></span></p>
  <pre>-- <o:p></o:p></pre>
  <pre>David Creasy<o:p></o:p></pre>
  <pre>Matrix Science<o:p></o:p></pre>
  <pre>64 Baker Street<o:p></o:p></pre>
  <pre>London W1U 7GB, UK<o:p></o:p></pre>
  <pre>Tel: +44 (0)20 7486 1050<o:p></o:p></pre>
  <pre>Fax: +44 (0)20 7224 1344<o:p></o:p></pre>
  <pre><o:p> </o:p></pre>
  <pre><a moz-do-not-send="true" href="mailto:dc...@ma...">dc...@ma...</a><o:p></o:p></pre>
  <pre><a moz-do-not-send="true" href="http://www.matrixscience.com">http://www.matrixscience.com</a><o:p></o:p></pre>
  <pre><o:p> </o:p></pre>
  <pre>Matrix Science Ltd. is registered in England and Wales<o:p></o:p></pre>
  <pre>Company number 3533898<o:p></o:p></pre>
  <pre><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;">
<hr align="center" size="4" width="90%">

  </pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre><o:p> </o:p></pre>
  <pre>-------------------------------------------------------------------------<o:p></o:p></pre>
  <pre>This SF.Net email is sponsored by the Moblin Your Move Developer's challenge<o:p></o:p></pre>
  <pre>Build the coolest Linux based applications with Moblin SDK &amp; win great prizes<o:p></o:p></pre>
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  <pre><a moz-do-not-send="true"
 href="http://moblin-contest.org/redirect.php?banner_id=100&amp;url=/">http://moblin-contest.org/redirect.php?banner_id=100&amp;url=/</a><o:p></o:p></pre>
  <pre><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;">
<hr align="center" size="4" width="90%">

  </pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre style="text-align: center;"><o:p> </o:p></pre>
  <pre><o:p> </o:p></pre>
  <pre>_______________________________________________<o:p></o:p></pre>
  <pre>Psidev-pi-dev mailing list<o:p></o:p></pre>
  <pre><a moz-do-not-send="true"
 href="mailto:Psi...@li...">Psi...@li...</a><o:p></o:p></pre>
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 href="https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev">https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev</a><o:p></o:p></pre>
  <pre>  <o:p></o:p></pre>
  </div>
  </div>
  </div>
  <pre wrap="">
<hr size="4" width="90%">
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK &amp; win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
<a class="moz-txt-link-freetext" href="http://moblin-contest.org/redirect.php?banner_id=100&url=/">http://moblin-contest.org/redirect.php?banner_id=100&amp;url=/</a></pre>
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  </pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">-- 
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344

<a class="moz-txt-link-abbreviated" href="mailto:dc...@ma...">dc...@ma...</a>
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Matrix Science Ltd. is registered in England and Wales
Company number 3533898</pre>
</body>
</html>

Re: [Psidev-pi-dev] FW: Spec doc

[Andreas B. <be...@in...>]

Hi David,

>  I've updated the Mascot_MSMS_example.axml,
>        <FragmentTolerance>
>          <pf:cvParam accession="PI:00404" name="absolut mass unit"
> value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton"
> unitCvRef="UO" /> <pf:cvParam accession="PI:00404" name="absolut mass unit"
> value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton"
> unitCvRef="UO" /> </FragmentTolerance>
>        <ParentTolerance>
>          <pf:cvParam accession="PI:00403" name="relative mass unit"
> value="0.1" cvRef="PSI-PI" unitAccession="UO:0000187" unitName="percent"
> unitCvRef="UO" /> <pf:cvParam accession="PI:00403" name="relative mass
> unit" value="0.1" cvRef="PSI-PI" unitAccession="UO:0000187"
> unitName="percent" unitCvRef="UO" /> </ParentTolerance>
Is there a reason to repeat the unit lines? I've added term UO:0000187 percent 
to the allowed ones, this is a synonym of parts per hundred, however 
separately listed in unit.obo...

>  but this doesn't validate:
The file still does not validate with some new errors, as you suggested ;)
Error: Name of CVTerm not correct: 'PI:00404 - absolut mass unit' should be 
'absolute mass unit'
Error: Violated mapping rule 'R17a' number of term repeats at element 
'/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ParentTolerance'
Error: Violated mapping rule 'R17b' number of term repeats at element 
'/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/FragmentTolerance'

Blame me, if you experience other unexpected results.

>  I'm also slightly concerned about PSI-PI group getting the wrong(?)
> reputation. Martin, could you change PI:00404 from being a brand of vodka
> to "absolute". Thanks. (I've still not installed OboEdit.)
(Maybe the CV and mapping file look much clearer with enough absolut)
@Martin: I've changed terms 403 and 404, added value-types and added 
percentage unit. Hopefully this merges with your local changes (if any).

Thanks,
A.


-- 
Div. for Simulation of Biological Systems, WSI, University of Tuebingen
Room C322, Sand 14, 72076 Tuebingen, Germany
phone: +49-7071-29-70461 fax: +49-7071-29-5152
http://www-bs.informatik.uni-tuebingen.de

Re: [Psidev-pi-dev] FW: Spec doc

[David C. <dc...@ma...>]

Hi Andreas,

 > (Maybe the CV and mapping file look much clearer with enough absolut)
I'm not sure why you can see double
CV entries for the fragment and parent tolerance ;)

So, originally we had:
<PlusValue   >
<MinusValue  >

Andy suggested:
Andreas can you add: “search tolerance plus value” and “search tolerance 
minus value” to the CV and mapping file and I’ll change the schema, does 
this seem reasonable to everyone…?

I looked in the mapping file and saw:
         <CvMappingRule id="R17a" 
cvElementPath="/psi-pi:AnalysisXML/psi-pi:AnalysisProtocolCollection/psi-pi:SpectrumIdentificationProtocol/psi-pi:ParentTolerance/pf:cvParam/@accession" 
requirementLevel="MUST"  scopePath="" cvTermsCombinationLogic="OR">
             <CvTerm termAccession="PI:00402" useTermName="false" 
useTerm="false" termName="mass units" isRepeatable="false" 
allowChildren="true" cvIdentifierRef="PSI-PI" />
         </CvMappingRule>


and then must have forgotten what we were trying to do....

So, I think that we must add the two CV terms Andy originally suggested?
Could you do that please? (I don't think Martin will be doing any edits).

Thanks,

David

Andreas Bertsch wrote:
> Hi David,
> 
>>  I've updated the Mascot_MSMS_example.axml,
>>        <FragmentTolerance>
>>          <pf:cvParam accession="PI:00404" name="absolut mass unit"
>> value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton"
>> unitCvRef="UO" /> <pf:cvParam accession="PI:00404" name="absolut mass unit"
>> value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton"
>> unitCvRef="UO" /> </FragmentTolerance>
>>        <ParentTolerance>
>>          <pf:cvParam accession="PI:00403" name="relative mass unit"
>> value="0.1" cvRef="PSI-PI" unitAccession="UO:0000187" unitName="percent"
>> unitCvRef="UO" /> <pf:cvParam accession="PI:00403" name="relative mass
>> unit" value="0.1" cvRef="PSI-PI" unitAccession="UO:0000187"
>> unitName="percent" unitCvRef="UO" /> </ParentTolerance>
> Is there a reason to repeat the unit lines? I've added term UO:0000187 percent 
> to the allowed ones, this is a synonym of parts per hundred, however 
> separately listed in unit.obo...
> 
>>  but this doesn't validate:
> The file still does not validate with some new errors, as you suggested ;)
> Error: Name of CVTerm not correct: 'PI:00404 - absolut mass unit' should be 
> 'absolute mass unit'
> Error: Violated mapping rule 'R17a' number of term repeats at element 
> '/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ParentTolerance'
> Error: Violated mapping rule 'R17b' number of term repeats at element 
> '/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/FragmentTolerance'
> 
> Blame me, if you experience other unexpected results.
> 
>>  I'm also slightly concerned about PSI-PI group getting the wrong(?)
>> reputation. Martin, could you change PI:00404 from being a brand of vodka
>> to "absolute". Thanks. (I've still not installed OboEdit.)
> (Maybe the CV and mapping file look much clearer with enough absolut)
> @Martin: I've changed terms 403 and 404, added value-types and added 
> percentage unit. Hopefully this merges with your local changes (if any).
> 
> Thanks,
> A.
> 
> 

-- 
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344

dc...@ma...
http://www.matrixscience.com

Matrix Science Ltd. is registered in England and Wales
Company number 3533898

Re: [Psidev-pi-dev] FW: Spec doc

[Andreas B. <be...@in...>]

Hi David,

> Andy suggested:
> Andreas can you add: “search tolerance plus value” and “search tolerance
> minus value” to the CV and mapping file and I’ll change the schema, does
> this seem reasonable to everyone…?
Sorry, that is my fault, I have overlooked this structure. I have added the cv 
two terms, 412 and 413, plus and minus value. The Mascot MSMS example would 
look like this using the new terms.

      <FragmentTolerance>
        <pf:cvParam accession="PI:00412" name="search tolerance plus value" 
value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton" 
unitCvRef="UO" />
        <pf:cvParam accession="PI:00413" name="search tolerance minus value" 
value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton" 
unitCvRef="UO" />
      </FragmentTolerance>
      <ParentTolerance>
        <pf:cvParam accession="PI:00412" name="search tolerance plus value" 
value="0.1" cvRef="PSI-PI" unitAccession="UO:0000187" unitName="percent" 
unitCvRef="UO" />
        <pf:cvParam accession="PI:00413" name="search tolerance minus value" 
value="0.1" cvRef="PSI-PI" unitAccession="UO:0000187" unitName="percent" 
unitCvRef="UO" />
      </ParentTolerance>

I have also updated the mapping file accordingly. Now two values (exactly two 
terms) are required, one plus and one minus value. The units are directly 
associated with the two terms. So the "mass units" tree becomes obsolete 
(absolut(e)ly), and I would suggest to delete it, if there is no good reason 
to keep it. I also think that a distinction into absolute and relative is not 
necessary as it is clear by specifying the units.

> So, I think that we must add the two CV terms Andy originally suggested?
> Could you do that please? (I don't think Martin will be doing any edits).
Done. Semantic validator is also updated. Sorry for any inconvencience.

Thanks,
A.


-- 
Div. for Simulation of Biological Systems, WSI, University of Tuebingen
Room C322, Sand 14, 72076 Tuebingen, Germany
phone: +49-7071-29-70461 fax: +49-7071-29-5152
http://www-bs.informatik.uni-tuebingen.de

Re: [Psidev-pi-dev] FW: Spec doc

[Jones, A. <And...@li...>]

Hi all,

New spec doc uploaded by SVN: 

Several updates, inserted new auto-generated documentation, section on
spectrumID, section on internal ions, added listing of example files.

Hopefully the images should appear this time, let me know if they don't. Can
everyone take a look in particular at the comments in the margin. Also we need a
more complete list of the contributors at the end, please mail me names of
people to add.

Cheers
Andy








> -----Original Message-----
> From: Andreas Bertsch [mailto:be...@in...]
> Sent: 04 December 2008 15:10
> To: David Creasy
> Cc: psi...@li...
> Subject: Re: [Psidev-pi-dev] FW: Spec doc
> 
> Hi David,
> 
> > Andy suggested:
> > Andreas can you add: “search tolerance plus value” and “search tolerance
> > minus value” to the CV and mapping file and I’ll change the schema, does
> > this seem reasonable to everyone…?
> Sorry, that is my fault, I have overlooked this structure. I have added the cv
> two terms, 412 and 413, plus and minus value. The Mascot MSMS example would
> look like this using the new terms.
> 
>       <FragmentTolerance>
>         <pf:cvParam accession="PI:00412" name="search tolerance plus value"
> value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton"
> unitCvRef="UO" />
>         <pf:cvParam accession="PI:00413" name="search tolerance minus value"
> value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton"
> unitCvRef="UO" />
>       </FragmentTolerance>
>       <ParentTolerance>
>         <pf:cvParam accession="PI:00412" name="search tolerance plus value"
> value="0.1" cvRef="PSI-PI" unitAccession="UO:0000187" unitName="percent"
> unitCvRef="UO" />
>         <pf:cvParam accession="PI:00413" name="search tolerance minus value"
> value="0.1" cvRef="PSI-PI" unitAccession="UO:0000187" unitName="percent"
> unitCvRef="UO" />
>       </ParentTolerance>
> 
> I have also updated the mapping file accordingly. Now two values (exactly two
> terms) are required, one plus and one minus value. The units are directly
> associated with the two terms. So the "mass units" tree becomes obsolete
> (absolut(e)ly), and I would suggest to delete it, if there is no good reason
> to keep it. I also think that a distinction into absolute and relative is not
> necessary as it is clear by specifying the units.
> 
> > So, I think that we must add the two CV terms Andy originally suggested?
> > Could you do that please? (I don't think Martin will be doing any edits).
> Done. Semantic validator is also updated. Sorry for any inconvencience.
> 
> Thanks,
> A.
> 
> 
> --
> Div. for Simulation of Biological Systems, WSI, University of Tuebingen
> Room C322, Sand 14, 72076 Tuebingen, Germany
> phone: +49-7071-29-70461 fax: +49-7071-29-5152
> http://www-bs.informatik.uni-tuebingen.de
> 
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

Re: [Psidev-pi-dev] FW: Spec doc

[David C. <dc...@ma...>]

Hi Andreas,

Andreas Bertsch wrote:
> Hi David,
> 
>> Andy suggested:
>> Andreas can you add: “search tolerance plus value” and “search tolerance
>> minus value” to the CV and mapping file and I’ll change the schema, does
>> this seem reasonable to everyone…?
> Sorry, that is my fault, I have overlooked this structure. I have added the cv 
> two terms, 412 and 413, plus and minus value. The Mascot MSMS example would 
> look like this using the new terms.
Thanks. I've updated the Mascot examples, and all seem to validate 
properly now.

> 
> I have also updated the mapping file accordingly. Now two values (exactly two 
> terms) are required, one plus and one minus value. The units are directly 
> associated with the two terms. So the "mass units" tree becomes obsolete 
> (absolut(e)ly), and I would suggest to delete it, if there is no good reason 
> to keep it. 
Yes, I would think that we can delete these.

 > I also think that a distinction into absolute and relative is not
 > necessary as it is clear by specifying the units.
Agree.

I've just one remaining validation error:

Error: CV term used in invalid element: 'PI:00410 - translation start 
codons' at element 
'/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/DatabaseTranslation/TranslationTable'

I think that the mapping is wrong - or maybe you need a new parent term 
for this and PI:00025?

David

Re: [Psidev-pi-dev] FW: Spec doc

[Eric D. <ede...@sy...>]

I have refreshed the on-line docs at:

http://www.peptideatlas.org/tmp/AnalysisXML_working.html

I notice that several of the xxxx_ref attributes do not have definitions.

Regards,
Eric


> -----Original Message-----
> From: David Creasy [mailto:dc...@ma...]
> Sent: Thursday, December 04, 2008 9:50 AM
> To: Andreas Bertsch
> Cc: psi...@li...
> Subject: Re: [Psidev-pi-dev] FW: Spec doc
> 
> Hi Andreas,
> 
> Andreas Bertsch wrote:
> > Hi David,
> >
> >> Andy suggested:
> >> Andreas can you add: "search tolerance plus value" and "search
> tolerance
> >> minus value" to the CV and mapping file and I'll change the schema,
> does
> >> this seem reasonable to everyone.?
> > Sorry, that is my fault, I have overlooked this structure. I have added
> the cv
> > two terms, 412 and 413, plus and minus value. The Mascot MSMS example
> would
> > look like this using the new terms.
> Thanks. I've updated the Mascot examples, and all seem to validate
> properly now.
> 
> >
> > I have also updated the mapping file accordingly. Now two values
> (exactly two
> > terms) are required, one plus and one minus value. The units are
> directly
> > associated with the two terms. So the "mass units" tree becomes obsolete
> > (absolut(e)ly), and I would suggest to delete it, if there is no good
> reason
> > to keep it.
> Yes, I would think that we can delete these.
> 
>  > I also think that a distinction into absolute and relative is not
>  > necessary as it is clear by specifying the units.
> Agree.
> 
> I've just one remaining validation error:
> 
> Error: CV term used in invalid element: 'PI:00410 - translation start
> codons' at element
> '/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/Da
> tabaseTranslation/TranslationTable'
> 
> I think that the mapping is wrong - or maybe you need a new parent term
> for this and PI:00025?
> 
> David
> 
> 
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the
> world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev

Re: [Psidev-pi-dev] FW: Spec doc

[Pierre-Alain B. <pie...@is...>]

Just a question about these tolerances:
if one need to specify a union of 2 sets of tolerances, such as 200ppm 
and 0.1Da (which means 200ppm with a minimum of 0.1Da), can one just 
have twice the pair of tolerances? for instance:

      <FragmentTolerance>
        <pf:cvParam accession="PI:00412" name="search tolerance plus value" 
value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton" 
unitCvRef="UO" />
        <pf:cvParam accession="PI:00412" name="search tolerance plus value" 
value="500" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="ppm" 
unitCvRef="UO" />
        <pf:cvParam accession="PI:00413" name="search tolerance minus value" 
value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton" 
unitCvRef="UO" />
        <pf:cvParam accession="PI:00412" name="search tolerance plus value" 
value="500" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="ppm" 
unitCvRef="UO" />
      </FragmentTolerance>


Pierre-Alain


Andreas Bertsch wrote:
> Hi David,
>
>   
>> Andy suggested:
>> Andreas can you add: “search tolerance plus value” and “search tolerance
>> minus value” to the CV and mapping file and I’ll change the schema, does
>> this seem reasonable to everyone…?
>>     
> Sorry, that is my fault, I have overlooked this structure. I have added the cv 
> two terms, 412 and 413, plus and minus value. The Mascot MSMS example would 
> look like this using the new terms.
>
>       <FragmentTolerance>
>         <pf:cvParam accession="PI:00412" name="search tolerance plus value" 
> value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton" 
> unitCvRef="UO" />
>         <pf:cvParam accession="PI:00413" name="search tolerance minus value" 
> value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton" 
> unitCvRef="UO" />
>       </FragmentTolerance>
>       <ParentTolerance>
>         <pf:cvParam accession="PI:00412" name="search tolerance plus value" 
> value="0.1" cvRef="PSI-PI" unitAccession="UO:0000187" unitName="percent" 
> unitCvRef="UO" />
>         <pf:cvParam accession="PI:00413" name="search tolerance minus value" 
> value="0.1" cvRef="PSI-PI" unitAccession="UO:0000187" unitName="percent" 
> unitCvRef="UO" />
>       </ParentTolerance>
>
> I have also updated the mapping file accordingly. Now two values (exactly two 
> terms) are required, one plus and one minus value. The units are directly 
> associated with the two terms. So the "mass units" tree becomes obsolete 
> (absolut(e)ly), and I would suggest to delete it, if there is no good reason 
> to keep it. I also think that a distinction into absolute and relative is not 
> necessary as it is clear by specifying the units.
>
>   
>> So, I think that we must add the two CV terms Andy originally suggested?
>> Could you do that please? (I don't think Martin will be doing any edits).
>>     
> Done. Semantic validator is also updated. Sorry for any inconvencience.
>
> Thanks,
> A.
>
>
>   

Re: [Psidev-pi-dev] FW: Spec doc

[Andreas B. <be...@in...>]

Hi Pierre-Alain,

> Just a question about these tolerances:
> if one need to specify a union of 2 sets of tolerances, such as 200ppm
> and 0.1Da (which means 200ppm with a minimum of 0.1Da), can one just
> have twice the pair of tolerances? for instance:
>       <FragmentTolerance>
>         <pf:cvParam accession="PI:00412" name="search tolerance plus value"
> value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton"
> unitCvRef="UO" />
>         <pf:cvParam accession="PI:00412" name="search tolerance plus value"
> value="500" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="ppm"
> unitCvRef="UO" />
>         <pf:cvParam accession="PI:00413" name="search tolerance minus
> value" value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221"
> unitName="dalton" unitCvRef="UO" />
>         <pf:cvParam accession="PI:00412" name="search tolerance plus value"
> value="500" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="ppm"
> unitCvRef="UO" />
>       </FragmentTolerance>
At the moment this cannot be done. And just repeating the terms would be 
confusing in my opinion. The meaning that one is a minimum mass tolerance and 
the other one is the one used if it is greater than the threshold would not be 
directly obvious while reading the file. If we want to support such constructs 
we need schema changes here, I think. Are there any search engines which allow 
for such a specification of the tolerance?

Cheers,
A.



-- 
Div. for Simulation of Biological Systems, WSI, University of Tuebingen
Room C322, Sand 14, 72076 Tuebingen, Germany
phone: +49-7071-29-70461 fax: +49-7071-29-5152
http://www-bs.informatik.uni-tuebingen.de

Re: [Psidev-pi-dev] FW: Spec doc

[Pierre-Alain B. <pie...@is...>]

Yes, there are tools using more complex rules than only one global metrics:

Phenyx uses this for the fragments in some scoring models (although not 
specified by the user),
Aldente has the option for PMF
Profound proposes for PMF two separate tolerances for data submitted 
with monoisotopic or average precision (a combination is possible)
MSTag (from ProteinProspector) has a "systematic error" value with the 
same unit as the parent tolerance one
MS-Fit has a similar option
Mascot allows "local" tolerance values if the input file is mgf (at 
least the format allows to specify specific tolerances for a given spectrum)

I believe that now we have to live with a first version that considers 
only one simple metrics, particularly if including the complexity would 
require a schema change.

Pierre-Alain


Andreas Bertsch wrote:
> Hi Pierre-Alain,
>
>   
>> Just a question about these tolerances:
>> if one need to specify a union of 2 sets of tolerances, such as 200ppm
>> and 0.1Da (which means 200ppm with a minimum of 0.1Da), can one just
>> have twice the pair of tolerances? for instance:
>>       <FragmentTolerance>
>>         <pf:cvParam accession="PI:00412" name="search tolerance plus value"
>> value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton"
>> unitCvRef="UO" />
>>         <pf:cvParam accession="PI:00412" name="search tolerance plus value"
>> value="500" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="ppm"
>> unitCvRef="UO" />
>>         <pf:cvParam accession="PI:00413" name="search tolerance minus
>> value" value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221"
>> unitName="dalton" unitCvRef="UO" />
>>         <pf:cvParam accession="PI:00412" name="search tolerance plus value"
>> value="500" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="ppm"
>> unitCvRef="UO" />
>>       </FragmentTolerance>
>>     
> At the moment this cannot be done. And just repeating the terms would be 
> confusing in my opinion. The meaning that one is a minimum mass tolerance and 
> the other one is the one used if it is greater than the threshold would not be 
> directly obvious while reading the file. If we want to support such constructs 
> we need schema changes here, I think. Are there any search engines which allow 
> for such a specification of the tolerance?
>
> Cheers,
> A.
>
>
>
>